rs6850606

Variant names:

• chr4-42862679-G-A
• rs6850606

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 0.459 in 151,832 control chromosomes in the GnomAD database, including 16,475 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 0.46 (16475 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 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: 0.459 AC: 69679 AN: 151712 Hom.: 16470 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.459 AC: 69718 AN: 151832 Hom.: 16475 Cov.: 31 AF XY: 0.459 AC XY: 34045 AN XY: 74192

African (AFR) AF: 0.401 AC: 16616 AN: 41404

American (AMR) AF: 0.432 AC: 6591 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2018 AN: 3462

East Asian (EAS) AF: 0.266 AC: 1369 AN: 5150

South Asian (SAS) AF: 0.480 AC: 2306 AN: 4804

European-Finnish (FIN) AF: 0.527 AC: 5545 AN: 10526

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33816 AN: 67922

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.488 Hom.: 9814

Bravo AF: 0.447

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.036
DANN	Benign	0.66
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6850606; hg19: chr4-42864696;