rs7921462

Variant names:

• chr10-100083383-T-C
• rs7921462

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 0.0757 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0758 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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.0478

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.0412

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.0655

Gnomad4 OTH AF: 0.0751

Alfa AF: 0.0675 Hom.: 203

Bravo AF: 0.0736

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7921462; hg19: chr10-101843140;