6-137912948-G-C

Variant names:

• chr6-137912948-G-C
• rs4896303

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.49 in 152,010 control chromosomes in the GnomAD database, including 21,765 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 0.49 (21765 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74338 AN: 151892 Hom.: 21707 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.490 AC: 74460 AN: 152010 Hom.: 21765 Cov.: 32 AF XY: 0.486 AC XY: 36103 AN XY: 74292

African (AFR) AF: 0.824 AC: 34181 AN: 41484

American (AMR) AF: 0.446 AC: 6816 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3472

East Asian (EAS) AF: 0.150 AC: 774 AN: 5164

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4808

European-Finnish (FIN) AF: 0.368 AC: 3882 AN: 10542

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24097 AN: 67952

Other (OTH) AF: 0.452 AC: 954 AN: 2110

Alfa AF: 0.233 Hom.: 477

Bravo AF: 0.508

Asia WGS AF: 0.339 AC: 1182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.54
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs4896303; hg19: chr6-138234085;