rs317105

Variant names:

• chr6-153222860-G-A
• rs317105

Your query was ambiguous. Multiple possible variants found:

• chr6-153222860-G-A
• chr6-153222860-G-C
• chr6-153222860-G-T

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 0.404 in 152,032 control chromosomes in the GnomAD database, including 13,493 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 0.40 (13493 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61435 AN: 151914 Hom.: 13494 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.404 AC: 61440 AN: 152032 Hom.: 13493 Cov.: 32 AF XY: 0.405 AC XY: 30110 AN XY: 74288

African (AFR) AF: 0.226 AC: 9387 AN: 41484

American (AMR) AF: 0.388 AC: 5932 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1514 AN: 3472

East Asian (EAS) AF: 0.459 AC: 2372 AN: 5170

South Asian (SAS) AF: 0.459 AC: 2210 AN: 4816

European-Finnish (FIN) AF: 0.476 AC: 5021 AN: 10552

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33419 AN: 67952

Other (OTH) AF: 0.426 AC: 899 AN: 2110

Alfa AF: 0.463 Hom.: 25781

Bravo AF: 0.387

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.36
DANN	Benign	0.41
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs317105; hg19: chr6-153543995;