rs1885629

Variant names:

• chr6-153941759-T-C
• rs1885629

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 0.225 in 152,164 control chromosomes in the GnomAD database, including 4,260 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 0.22 (4260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.832
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.382 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: 0.225 AC: 34174 AN: 152046 Hom.: 4252 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.225 AC: 34187 AN: 152164 Hom.: 4260 Cov.: 32 AF XY: 0.233 AC XY: 17341 AN XY: 74392

African (AFR) AF: 0.144 AC: 5974 AN: 41540

American (AMR) AF: 0.390 AC: 5963 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3472

East Asian (EAS) AF: 0.326 AC: 1686 AN: 5164

South Asian (SAS) AF: 0.386 AC: 1858 AN: 4816

European-Finnish (FIN) AF: 0.237 AC: 2510 AN: 10580

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14422 AN: 67978

Other (OTH) AF: 0.256 AC: 542 AN: 2114

Alfa AF: 0.233 Hom.: 802

Bravo AF: 0.228

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.64
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs1885629; hg19: chr6-154262894; COSMIC: COSV107510656;