rs1075724

Variant names:

• chr10-128126730-T-C
• rs1075724

Your query was ambiguous. Multiple possible variants found:

• chr10-128126730-T-C
• chr10-128126730-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.341

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1075724; hg19: chr10-129924994;