rs7921462

Variant names:

• chr10-100083383-T-C
• rs7921462

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 0.0757 in 152,276 control chromosomes in the GnomAD database, including 490 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 0.076 (490 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0758 AC: 11528 AN: 152158 Hom.: 489 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.0418

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0655

Gnomad OTH AF: 0.0759

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

GnomAD4 genome AF: 0.0757 AC: 11530 AN: 152276 Hom.: 490 Cov.: 33 AF XY: 0.0763 AC XY: 5683 AN XY: 74452

African (AFR) AF: 0.103 AC: 4292 AN: 41550

American (AMR) AF: 0.0478 AC: 732 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0602 AC: 209 AN: 3470

East Asian (EAS) AF: 0.0628 AC: 326 AN: 5190

South Asian (SAS) AF: 0.0412 AC: 199 AN: 4832

European-Finnish (FIN) AF: 0.103 AC: 1090 AN: 10582

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0655 AC: 4455 AN: 68028

Other (OTH) AF: 0.0751 AC: 159 AN: 2116

Alfa AF: 0.0678 Hom.: 218

Bravo AF: 0.0736

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.37
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs7921462; hg19: chr10-101843140;