rs10493592

Positions:

• chr1-76727974-C-A
• chr1-76727974-C-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 0.152 in 152,140 control chromosomes in the GnomAD database, including 2,831 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 0.15 (2831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.151 AC: 23017 AN: 152022 Hom.: 2818 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0747

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.152 AC: 23062 AN: 152140 Hom.: 2831 Cov.: 32 AF XY: 0.150 AC XY: 11134 AN XY: 74394

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.0743

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0587

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.153

Alfa AF: 0.0920 Hom.: 245

Bravo AF: 0.160

Asia WGS AF: 0.197 AC: 681 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	0.92
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493592; hg19: chr1-77193659;