rs10746514

Positions:

• chr1-232110281-G-A
• chr1-232110281-G-C

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 0.38 in 151,964 control chromosomes in the GnomAD database, including 11,434 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 (11434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.771

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 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: 0.380 AC: 57769 AN: 151846 Hom.: 11419 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.380 AC: 57817 AN: 151964 Hom.: 11434 Cov.: 32 AF XY: 0.379 AC XY: 28162 AN XY: 74264

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.414

Alfa AF: 0.422 Hom.: 20621

Bravo AF: 0.374

Asia WGS AF: 0.386 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10746514; hg19: chr1-232246027;