rs1544210

Variant names:

• chr10-92728044-G-A
• rs1544210

Your query was ambiguous. Multiple possible variants found:

• chr10-92728044-G-A
• chr10-92728044-G-T

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 0.392 in 151,894 control chromosomes in the GnomAD database, including 13,182 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 0.39 (13182 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.880
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 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: 0.392 AC: 59565 AN: 151776 Hom.: 13184 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.392 AC: 59578 AN: 151894 Hom.: 13182 Cov.: 32 AF XY: 0.396 AC XY: 29374 AN XY: 74196

African (AFR) AF: 0.215 AC: 8904 AN: 41448

American (AMR) AF: 0.432 AC: 6601 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3470

East Asian (EAS) AF: 0.137 AC: 709 AN: 5182

South Asian (SAS) AF: 0.331 AC: 1589 AN: 4806

European-Finnish (FIN) AF: 0.544 AC: 5716 AN: 10514

Middle Eastern (MID) AF: 0.510 AC: 148 AN: 290

European-Non Finnish (NFE) AF: 0.493 AC: 33451 AN: 67904

Other (OTH) AF: 0.412 AC: 869 AN: 2108

Alfa AF: 0.422 Hom.: 1841

Bravo AF: 0.375

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.52
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs1544210; hg19: chr10-94487801;