rs10737909

chr1-15222140-G-T

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 0.457 in 151,804 control chromosomes in the GnomAD database, including 16,765 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 0.46 (16765 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69310 AN: 151684 Hom.: 16772 Cov.: 30

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.457 AC: 69321 AN: 151804 Hom.: 16765 Cov.: 30 AF XY: 0.449 AC XY: 33318 AN XY: 74156

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.490

Alfa AF: 0.496 Hom.: 6174

Bravo AF: 0.447

Asia WGS AF: 0.429 AC: 1494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.11
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10737909; hg19: chr1-15548636;