rs2505998

chr10-43075477-A-Gchr10-43075477-A-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 0.792 in 152,150 control chromosomes in the GnomAD database, including 48,774 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 0.79 (48774 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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: 0.792 AC: 120360 AN: 152032 Hom.: 48707 Cov.: 33

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.792 AC: 120494 AN: 152150 Hom.: 48774 Cov.: 33 AF XY: 0.784 AC XY: 58308 AN XY: 74348

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.778

Alfa AF: 0.745 Hom.: 10046

Bravo AF: 0.811

Asia WGS AF: 0.650 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.33
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505998; hg19: chr10-43570925;