chr10-123661474-T-A

Variant names:

• chr10-123661474-T-A
• rs1123012

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 0.401 in 152,058 control chromosomes in the GnomAD database, including 12,754 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 0.40 (12754 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.352
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.401 AC: 60913 AN: 151940 Hom.: 12748 Cov.: 33

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.401 AC: 60950 AN: 152058 Hom.: 12754 Cov.: 33 AF XY: 0.406 AC XY: 30163 AN XY: 74318

African (AFR) AF: 0.298 AC: 12377 AN: 41486

American (AMR) AF: 0.425 AC: 6502 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1318 AN: 3468

East Asian (EAS) AF: 0.621 AC: 3211 AN: 5174

South Asian (SAS) AF: 0.453 AC: 2174 AN: 4804

European-Finnish (FIN) AF: 0.521 AC: 5500 AN: 10558

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28494 AN: 67962

Other (OTH) AF: 0.403 AC: 851 AN: 2110

Alfa AF: 0.406 Hom.: 1581

Bravo AF: 0.393

Asia WGS AF: 0.528 AC: 1835 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	0.28
DANN	Benign	0.53
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1123012; hg19: chr10-125420990;