chr6-152897587-C-A

Variant names:

• chr6-152897587-C-A
• rs555985

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 0.539 in 151,934 control chromosomes in the GnomAD database, including 22,623 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 0.54 (22623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.594
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.64 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: 0.539 AC: 81821 AN: 151814 Hom.: 22587 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.539 AC: 81912 AN: 151934 Hom.: 22623 Cov.: 32 AF XY: 0.542 AC XY: 40218 AN XY: 74222

African (AFR) AF: 0.637 AC: 26387 AN: 41424

American (AMR) AF: 0.619 AC: 9465 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1459 AN: 3468

East Asian (EAS) AF: 0.504 AC: 2594 AN: 5146

South Asian (SAS) AF: 0.660 AC: 3179 AN: 4820

European-Finnish (FIN) AF: 0.461 AC: 4844 AN: 10506

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.475 AC: 32256 AN: 67972

Other (OTH) AF: 0.517 AC: 1090 AN: 2110

Alfa AF: 0.515 Hom.: 3578

Bravo AF: 0.552

Asia WGS AF: 0.605 AC: 2100 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.42
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs555985; hg19: chr6-153218722; COSMIC: COSV69403971;