rs10737909

Variant names:

• chr1-15222140-G-T
• rs10737909

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.314 AC: 13001 AN: 41394

American (AMR) AF: 0.403 AC: 6154 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1886 AN: 3468

East Asian (EAS) AF: 0.401 AC: 2056 AN: 5122

South Asian (SAS) AF: 0.539 AC: 2592 AN: 4810

European-Finnish (FIN) AF: 0.419 AC: 4391 AN: 10482

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37556 AN: 67952

Other (OTH) AF: 0.490 AC: 1033 AN: 2108

Alfa AF: 0.495 Hom.: 10887

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10737909; hg19: chr1-15548636;