dbSNP rs2413687: NFAM1:c.*1468A>G (chr22-42383693-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145912.8(NFAM1):c.*1468A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,654 control chromosomes in the GnomAD database, including 33,854 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.64 ( 33793 hom., cov: 33)

Exomes 𝑓: 0.49 ( 61 hom. )

Consequence

NFAM1
NM_145912.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.96

Publications

5 publications found

Variant links:

Genes affected

NFAM1 (HGNC:29872): (NFAT activating protein with ITAM motif 1) The protein encoded by this gene is a type I membrane receptor that activates cytokine gene promoters such as the IL-13 and TNF-alpha promoters. The encoded protein contains an immunoreceptor tyrosine-based activation motif (ITAM) and is thought to regulate the signaling and development of B-cells. [provided by RefSeq, Jul 2008]

NFAM1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145912.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
NFAM1	NM_145912.8	MANE Select	c.*1468A>G	3_prime_UTR	Exon 6 of 6	NP_666017.1
NFAM1	NM_001371362.1		c.*1468A>G	3_prime_UTR	Exon 8 of 8	NP_001358291.1
NFAM1	NM_001318323.3		c.*1571A>G	3_prime_UTR	Exon 5 of 5	NP_001305252.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFAM1	ENST00000329021.10	TSL:1 MANE Select	c.*1468A>G		3_prime_UTR	Exon 6 of 6	ENSP00000333680.5
	NFAM1	ENST00000968877.1		c.*1468A>G		3_prime_UTR	Exon 5 of 5	ENSP00000638936.1

Frequencies

GnomAD3 genomes

AF:

0.644

AC:

97968

AN:

152024

Hom.:

33724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.902

Gnomad AMI

AF:

0.612

Gnomad AMR

AF:

0.658

Gnomad ASJ

AF:

0.589

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.655

Gnomad FIN

AF:

0.461

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.529

Gnomad OTH

AF:

0.623

GnomAD4 exome

AF:

0.488

AC:

250

AN:

512

Hom.:

Cov.:

AF XY:

0.478

AC XY:

154

AN XY:

322

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.486

AC:

205

AN:

422

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.473

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.448

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.645

AC:

98099

AN:

152142

Hom.:

33793

Cov.:

AF XY:

0.639

AC XY:

47532

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.902

AC:

37485

AN:

41546

American (AMR)

AF:

0.658

AC:

10058

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.589

AC:

2043

AN:

3470

East Asian (EAS)

AF:

0.472

AC:

2431

AN:

5146

South Asian (SAS)

AF:

0.656

AC:

3165

AN:

4828

European-Finnish (FIN)

AF:

0.461

AC:

4887

AN:

10594

Middle Eastern (MID)

AF:

0.626

AC:

184

AN:

294

European-Non Finnish (NFE)

AF:

0.529

AC:

35967

AN:

67962

Other (OTH)

AF:

0.628

AC:

1323

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1621

3241

4862

6482

8103

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

768

1536

2304

3072

3840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.378

Hom.:

774

Bravo

AF:

0.672

Asia WGS

AF:

0.633

AC:

2205

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.64

(source)

DANN

Benign

0.42

PhyloP100

-2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over