rs6910391

Variant names:

• chr6-100477898-T-C
• rs6910391

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 0.487 in 152,016 control chromosomes in the GnomAD database, including 18,263 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 0.49 (18263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 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: 0.487 AC: 74011 AN: 151898 Hom.: 18251 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.487 AC: 74043 AN: 152016 Hom.: 18263 Cov.: 32 AF XY: 0.488 AC XY: 36232 AN XY: 74316

African (AFR) AF: 0.454 AC: 18793 AN: 41430

American (AMR) AF: 0.427 AC: 6525 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1712 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1620 AN: 5188

South Asian (SAS) AF: 0.652 AC: 3130 AN: 4804

European-Finnish (FIN) AF: 0.524 AC: 5531 AN: 10564

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35179 AN: 67980

Other (OTH) AF: 0.494 AC: 1040 AN: 2106

Alfa AF: 0.489 Hom.: 12740

Bravo AF: 0.471

Asia WGS AF: 0.473 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.74
PhyloP100		0.0040

Splicing

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

Other links and lift over

dbSNP: rs6910391; hg19: chr6-100925774; COSMIC: COSV69415975;