rs7922744

Positions:

• chr10-105822379-T-A
• chr10-105822379-T-C

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 0.131 in 152,186 control chromosomes in the GnomAD database, including 3,677 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 0.13 (3677 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19851 AN: 152068 Hom.: 3659 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.0135

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.00263

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.131 AC: 19920 AN: 152186 Hom.: 3677 Cov.: 33 AF XY: 0.128 AC XY: 9527 AN XY: 74440

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.0461

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.00263

Gnomad4 NFE AF: 0.0141

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0119 Hom.: 17

Bravo AF: 0.144

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7922744; hg19: chr10-107582137;