rs10753575

Variant names:

• chr1-19837375-C-T
• rs10753575

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 0.638 in 151,850 control chromosomes in the GnomAD database, including 31,252 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 0.64 (31252 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.638 AC: 96860 AN: 151732 Hom.: 31226 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.600

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.638 AC: 96927 AN: 151850 Hom.: 31252 Cov.: 31 AF XY: 0.640 AC XY: 47524 AN XY: 74230

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.644

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.635

Alfa AF: 0.625 Hom.: 13588

Bravo AF: 0.639

Asia WGS AF: 0.847 AC: 2927 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10753575; hg19: chr1-20163868;