rs10826964

Positions:

• chr10-31568824-G-A
• chr10-31568824-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 0.232 in 152,130 control chromosomes in the GnomAD database, including 9,223 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 0.23 (9223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 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: 0.232 AC: 35288 AN: 152012 Hom.: 9189 Cov.: 32

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0720

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.232 AC: 35370 AN: 152130 Hom.: 9223 Cov.: 32 AF XY: 0.229 AC XY: 17064 AN XY: 74372

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0720

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0925 Hom.: 465

Bravo AF: 0.257

Asia WGS AF: 0.162 AC: 564 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10826964; hg19: chr10-31857752;