rs768676

chr10-44207233-T-Achr10-44207233-T-G

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 0.101 in 151,372 control chromosomes in the GnomAD database, including 1,463 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 0.10 (1463 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 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: 0.101 AC: 15329 AN: 151254 Hom.: 1458 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0659

Gnomad ASJ AF: 0.0693

Gnomad EAS AF: 0.00177

Gnomad SAS AF: 0.0487

Gnomad FIN AF: 0.0131

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0455

Gnomad OTH AF: 0.0922

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

GnomAD4 genome AF: 0.101 AC: 15355 AN: 151372 Hom.: 1463 Cov.: 33 AF XY: 0.0970 AC XY: 7171 AN XY: 73930

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.0658

Gnomad4 ASJ AF: 0.0693

Gnomad4 EAS AF: 0.00178

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.0131

Gnomad4 NFE AF: 0.0455

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0748 Hom.: 96

Bravo AF: 0.112

Asia WGS AF: 0.0370 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.5
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs768676; hg19: chr10-44702681;