10-122347530-T-C

Variant names:

• chr10-122347530-T-C
• rs11598094

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 0.247 in 152,098 control chromosomes in the GnomAD database, including 4,881 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 0.25 (4881 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.29 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: 0.247 AC: 37507 AN: 151978 Hom.: 4875 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.247 AC: 37517 AN: 152098 Hom.: 4881 Cov.: 32 AF XY: 0.244 AC XY: 18128 AN XY: 74352

African (AFR) AF: 0.173 AC: 7169 AN: 41482

American (AMR) AF: 0.227 AC: 3462 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1237 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1212 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4808

European-Finnish (FIN) AF: 0.209 AC: 2210 AN: 10596

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19973 AN: 67984

Other (OTH) AF: 0.282 AC: 595 AN: 2110

Alfa AF: 0.279 Hom.: 10944

Bravo AF: 0.246

Asia WGS AF: 0.242 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.75
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs11598094; hg19: chr10-124107045;