chr10-126876507-C-A

Variant names:

• chr10-126876507-C-A
• rs11245204

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 0.339 in 152,034 control chromosomes in the GnomAD database, including 10,320 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 (10320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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: 0.340 AC: 51585 AN: 151916 Hom.: 10325 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.339 AC: 51574 AN: 152034 Hom.: 10320 Cov.: 31 AF XY: 0.331 AC XY: 24558 AN XY: 74282

African (AFR) AF: 0.148 AC: 6152 AN: 41500

American (AMR) AF: 0.308 AC: 4693 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3468

East Asian (EAS) AF: 0.158 AC: 814 AN: 5148

South Asian (SAS) AF: 0.276 AC: 1332 AN: 4818

European-Finnish (FIN) AF: 0.365 AC: 3856 AN: 10564

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

European-Non Finnish (NFE) AF: 0.470 AC: 31957 AN: 67958

Other (OTH) AF: 0.368 AC: 777 AN: 2112

Alfa AF: 0.429 Hom.: 54970

Bravo AF: 0.326

Asia WGS AF: 0.252 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.52
DANN	Benign	0.48
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs11245204; hg19: chr10-128565076;