chr10-126878395-G-T

Variant names:

• chr10-126878395-G-T
• rs11599217

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 0.338 in 151,976 control chromosomes in the GnomAD database, including 10,253 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 0.34 (10253 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.289
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.464 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: 0.338 AC: 51391 AN: 151860 Hom.: 10257 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.338 AC: 51381 AN: 151976 Hom.: 10253 Cov.: 32 AF XY: 0.330 AC XY: 24471 AN XY: 74244

African (AFR) AF: 0.148 AC: 6136 AN: 41484

American (AMR) AF: 0.307 AC: 4687 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3464

East Asian (EAS) AF: 0.157 AC: 805 AN: 5134

South Asian (SAS) AF: 0.277 AC: 1331 AN: 4810

European-Finnish (FIN) AF: 0.364 AC: 3851 AN: 10568

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31812 AN: 67934

Other (OTH) AF: 0.367 AC: 774 AN: 2108

Alfa AF: 0.405 Hom.: 3357

Bravo AF: 0.325

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.57
DANN	Benign	0.78
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs11599217; hg19: chr10-128566964;