dbSNP rs6812193: FAM47E:c.871-236C>T (chr4-76277833-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001136570.3(FAM47E):c.871-236C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,046 control chromosomes in the GnomAD database, including 11,039 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 0.37 ( 11039 hom., cov: 32)

Consequence

FAM47E
NM_001136570.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0700

Publications

100 publications found

Variant links:

Genes affected

FAM47E (HGNC:34343): (family with sequence similarity 47 member E) Enables enzyme activator activity. Involved in positive regulation of histone methylation and protein localization to chromatin. Located in chromatin; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

FAM47E links:

FAM47E-STBD1 (HGNC:44667): (FAM47E-STBD1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring FAM47E (family with sequence similarity 47, member E) and STBD1 (starch binding domain 1) genes on chromosome 4. The read-through transcript encodes a protein that shares sequence identity with the upstream gene product but its C-terminal region is distinct due to frameshifts relative to the downstream gene. [provided by RefSeq, Jul 2011]

FAM47E-STBD1 links:

ENSG00000287401 (HGNC:):

ENSG00000287401 links:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136570.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM47E	NM_001136570.3	MANE Select	c.871-236C>T	intron	N/A	NP_001130042.1	Q6ZV65-3
FAM47E-STBD1	NM_001242939.2		c.871-236C>T	intron	N/A	NP_001229868.1
FAM47E	NM_001242936.1		c.577-236C>T	intron	N/A	NP_001229865.1	Q6ZV65-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FAM47E	ENST00000424749.7	TSL:5 MANE Select	c.871-236C>T	intron	N/A	ENSP00000409423.2	Q6ZV65-3
FAM47E-STBD1	ENST00000515604.5	TSL:2	c.871-236C>T	intron	N/A	ENSP00000422067.1
FAM47E	ENST00000853410.1		c.916-236C>T	intron	N/A	ENSP00000523469.1

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56711

AN:

151926

Hom.:

11034

Cov.:

show subpopulations

Gnomad AFR

AF:

0.447

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.0821

Gnomad SAS

AF:

0.289

Gnomad FIN

AF:

0.359

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.378

Gnomad OTH

AF:

0.370

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.373

AC:

56762

AN:

152046

Hom.:

11039

Cov.:

AF XY:

0.370

AC XY:

27475

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.446

AC:

18514

AN:

41476

American (AMR)

AF:

0.304

AC:

4646

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1073

AN:

3468

East Asian (EAS)

AF:

0.0823

AC:

426

AN:

5178

South Asian (SAS)

AF:

0.290

AC:

1396

AN:

4820

European-Finnish (FIN)

AF:

0.359

AC:

3793

AN:

10552

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.378

AC:

25715

AN:

67952

Other (OTH)

AF:

0.370

AC:

778

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1823

3646

5470

7293

9116

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

528

1056

1584

2112

2640

<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:

0.364

Hom.:

46504

Bravo

AF:

0.368

Asia WGS

AF:

0.209

AC:

729

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.5

(source)

DANN

Benign

0.61

PhyloP100

0.070

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over