dbSNP rs4716272: LOC105374955:n.147+455G>C (chr6-18497461-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_926548.3(LOC105374955):n.147+455G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,962 control chromosomes in the GnomAD database, including 3,167 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 0.20 ( 3167 hom., cov: 32)

Consequence

LOC105374955
XR_926548.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.442

Publications

2 publications found

Variant links:

Genes affected

LOC105374955 (HGNC:):

LOC105374955 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=-0.83).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374955	XR_926548.3 link	n.147+455G>C		intron_variant	Intron 1 of 3
LOC105374955	XR_926549.3 link	n.147+455G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.202

AC:

30686

AN:

151844

Hom.:

3171

Cov.:

show subpopulations

Gnomad AFR

AF:

0.186

Gnomad AMI

AF:

0.156

Gnomad AMR

AF:

0.226

Gnomad ASJ

AF:

0.147

Gnomad EAS

AF:

0.0862

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.210

Gnomad MID

AF:

0.245

Gnomad NFE

AF:

0.221

Gnomad OTH

AF:

0.207

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

GnomAD4 genome

AF:

0.202

AC:

30694

AN:

151962

Hom.:

3167

Cov.:

AF XY:

0.201

AC XY:

14948

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.185

AC:

7688

AN:

41446

American (AMR)

AF:

0.226

AC:

3456

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.147

AC:

509

AN:

3472

East Asian (EAS)

AF:

0.0859

AC:

443

AN:

5160

South Asian (SAS)

AF:

0.148

AC:

711

AN:

4810

European-Finnish (FIN)

AF:

0.210

AC:

2213

AN:

10520

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.221

AC:

15029

AN:

67960

Other (OTH)

AF:

0.204

AC:

432

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1240

2480

3720

4960

6200

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.209

Hom.:

421

Bravo

AF:

0.208

Asia WGS

AF:

0.118

AC:

410

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

8.3

(source)

DANN

Benign

0.61

PhyloP100

0.44

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over