chr10-128126730-T-C

Variant names:

• chr10-128126730-T-C
• rs1075724

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 0.381 in 151,834 control chromosomes in the GnomAD database, including 11,393 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 0.38 (11393 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 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: 0.381 AC: 57841 AN: 151716 Hom.: 11376 Cov.: 30

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.381 AC: 57893 AN: 151834 Hom.: 11393 Cov.: 30 AF XY: 0.378 AC XY: 28013 AN XY: 74184

African (AFR) AF: 0.483 AC: 19983 AN: 41398

American (AMR) AF: 0.301 AC: 4587 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1073 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2068 AN: 5144

South Asian (SAS) AF: 0.384 AC: 1847 AN: 4814

European-Finnish (FIN) AF: 0.315 AC: 3325 AN: 10542

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23839 AN: 67906

Other (OTH) AF: 0.341 AC: 721 AN: 2116

Alfa AF: 0.282 Hom.: 881

Bravo AF: 0.383

Asia WGS AF: 0.391 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.66
PhyloP100		-0.18
PromoterAI		-0.075	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1075724; hg19: chr10-129924994;