10-31596296-G-C

Position:

• chr10-31596296-G-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 0.748 in 151,914 control chromosomes in the GnomAD database, including 43,424 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 0.75 (43424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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 = 0.907 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: 0.747 AC: 113450 AN: 151792 Hom.: 43357 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.748 AC: 113577 AN: 151914 Hom.: 43424 Cov.: 32 AF XY: 0.740 AC XY: 54925 AN XY: 74218

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.631

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.712

Alfa AF: 0.600 Hom.: 1548

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
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: rs7092560; hg19: chr10-31885224;