rs10950821

Variant names:

• chr7-20607392-C-G
• rs10950821

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 0.353 in 151,802 control chromosomes in the GnomAD database, including 10,143 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 0.35 (10143 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.511
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.489 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: 0.352 AC: 53457 AN: 151684 Hom.: 10125 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.353 AC: 53531 AN: 151802 Hom.: 10143 Cov.: 31 AF XY: 0.362 AC XY: 26833 AN XY: 74168

African (AFR) AF: 0.472 AC: 19560 AN: 41406

American (AMR) AF: 0.354 AC: 5389 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 930 AN: 3464

East Asian (EAS) AF: 0.505 AC: 2610 AN: 5166

South Asian (SAS) AF: 0.370 AC: 1775 AN: 4792

European-Finnish (FIN) AF: 0.425 AC: 4470 AN: 10508

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17862 AN: 67920

Other (OTH) AF: 0.317 AC: 666 AN: 2104

Alfa AF: 0.321 Hom.: 1063

Bravo AF: 0.354

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.4
DANN	Benign	0.52
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10950821; hg19: chr7-20647015;