rs1339577

chr10-93724962-G-Achr10-93724962-G-Cchr10-93724962-G-T

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 0.8 in 151,486 control chromosomes in the GnomAD database, including 48,520 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 0.80 (48520 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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: 0.800 AC: 121060 AN: 151366 Hom.: 48483 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.800 AC: 121154 AN: 151486 Hom.: 48520 Cov.: 33 AF XY: 0.797 AC XY: 58984 AN XY: 74012

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.932

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.799

Alfa AF: 0.765 Hom.: 5961

Bravo AF: 0.802

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.12
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1339577; hg19: chr10-95484719;