rs195854

Variant names:

• chr6-98841599-T-A
• rs195854

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 0.659 in 148,486 control chromosomes in the GnomAD database, including 32,444 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 0.66 (32444 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 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: 0.659 AC: 97735 AN: 148386 Hom.: 32424 Cov.: 24

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.659 AC: 97786 AN: 148486 Hom.: 32444 Cov.: 24 AF XY: 0.662 AC XY: 47828 AN XY: 72294

African (AFR) AF: 0.595 AC: 23953 AN: 40254

American (AMR) AF: 0.737 AC: 11053 AN: 14992

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1785 AN: 3448

East Asian (EAS) AF: 0.706 AC: 3541 AN: 5018

South Asian (SAS) AF: 0.583 AC: 2713 AN: 4650

European-Finnish (FIN) AF: 0.737 AC: 7040 AN: 9556

Middle Eastern (MID) AF: 0.637 AC: 181 AN: 284

European-Non Finnish (NFE) AF: 0.677 AC: 45552 AN: 67310

Other (OTH) AF: 0.639 AC: 1323 AN: 2072

Alfa AF: 0.690 Hom.: 3475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	2.0
DANN	Benign	0.63
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs195854; hg19: chr6-99289475; COSMIC: COSV60409526;