rs6901854

Variant names:

• chr6-100484415-C-T
• rs6901854

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 0.523 in 152,042 control chromosomes in the GnomAD database, including 20,971 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 0.52 (20971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79538 AN: 151924 Hom.: 20955 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.523 AC: 79585 AN: 152042 Hom.: 20971 Cov.: 32 AF XY: 0.524 AC XY: 38950 AN XY: 74320

African (AFR) AF: 0.500 AC: 20704 AN: 41448

American (AMR) AF: 0.475 AC: 7254 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1751 AN: 3468

East Asian (EAS) AF: 0.366 AC: 1886 AN: 5154

South Asian (SAS) AF: 0.665 AC: 3209 AN: 4822

European-Finnish (FIN) AF: 0.542 AC: 5733 AN: 10576

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37411 AN: 67972

Other (OTH) AF: 0.526 AC: 1111 AN: 2112

Alfa AF: 0.550 Hom.: 13614

Bravo AF: 0.510

Asia WGS AF: 0.505 AC: 1758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	19
DANN	Benign	0.44
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs6901854; hg19: chr6-100932291; COSMIC: COSV60255606;