10-767486-C-T

Variant names:

• chr10-767486-C-T
• rs11253424

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.131 in 152,096 control chromosomes in the GnomAD database, including 1,755 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 0.13 (1755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19877 AN: 151978 Hom.: 1754 Cov.: 32

Gnomad AFR AF: 0.0328

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.0583

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.131 AC: 19884 AN: 152096 Hom.: 1755 Cov.: 32 AF XY: 0.130 AC XY: 9682 AN XY: 74332

African (AFR) AF: 0.0327 AC: 1358 AN: 41524

American (AMR) AF: 0.163 AC: 2496 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3468

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.0590 AC: 283 AN: 4796

European-Finnish (FIN) AF: 0.212 AC: 2229 AN: 10536

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12631 AN: 68000

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.159 Hom.: 5367

Bravo AF: 0.123

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.41
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11253424; hg19: chr10-813426;