10-43076540-T-C

Position:

• chr10-43076540-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 0.792 in 152,194 control chromosomes in the GnomAD database, including 48,817 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 (48817 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120446 AN: 152076 Hom.: 48750 Cov.: 35

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.754

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: 120580 AN: 152194 Hom.: 48817 Cov.: 35 AF XY: 0.785 AC XY: 58363 AN XY: 74382

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.778

Alfa AF: 0.767 Hom.: 5635

Bravo AF: 0.811

Asia WGS AF: 0.650 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2435366; hg19: chr10-43571988;