rs2243492

Positions:

• chr10-43353910-T-C
• chr10-43353910-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 0.779 in 152,130 control chromosomes in the GnomAD database, including 47,635 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 0.78 (47635 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.886 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: 0.780 AC: 118517 AN: 152012 Hom.: 47621 Cov.: 33

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.930

Gnomad AMR AF: 0.823

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.779 AC: 118568 AN: 152130 Hom.: 47635 Cov.: 33 AF XY: 0.774 AC XY: 57534 AN XY: 74352

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.613

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.819

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.816

Alfa AF: 0.850 Hom.: 33144

Bravo AF: 0.771

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.1
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2243492; hg19: chr10-43849358;