rs10805983

Variant names:

• chr6-73896985-T-C
• rs10805983

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0863

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0841

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.193

Alfa AF: 0.256 Hom.: 836

Bravo AF: 0.196

Asia WGS AF: 0.134 AC: 465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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