rs1339577

Variant names:

• chr10-93724962-G-A
• rs1339577

Your query was ambiguous. Multiple possible variants found:

• chr10-93724962-G-A
• chr10-93724962-G-C
• chr10-93724962-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;