rs10805983

Variant names:

• chr6-73896985-T-C
• rs10805983

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 0.209 in 152,126 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 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: 0.209 AC: 31721 AN: 152010 Hom.: 4001 Cov.: 33

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.209 AC: 31730 AN: 152126 Hom.: 4004 Cov.: 33 AF XY: 0.205 AC XY: 15247 AN XY: 74356

African (AFR) AF: 0.0863 AC: 3584 AN: 41536

American (AMR) AF: 0.179 AC: 2745 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3464

East Asian (EAS) AF: 0.0841 AC: 435 AN: 5172

South Asian (SAS) AF: 0.161 AC: 773 AN: 4816

European-Finnish (FIN) AF: 0.268 AC: 2827 AN: 10556

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20241 AN: 67968

Other (OTH) AF: 0.193 AC: 408 AN: 2112

Alfa AF: 0.250 Hom.: 838

Bravo AF: 0.196

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.66
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10805983; hg19: chr6-74606701; COSMIC: COSV69405137;