rs1152731

Variant names:

• chr1-10854750-A-G
• rs1152731

Your query was ambiguous. Multiple possible variants found:

• chr1-10854750-A-G
• chr1-10854750-A-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 0.253 in 152,076 control chromosomes in the GnomAD database, including 5,347 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 0.25 (5347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38417 AN: 151958 Hom.: 5347 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.253 AC: 38424 AN: 152076 Hom.: 5347 Cov.: 32 AF XY: 0.255 AC XY: 18973 AN XY: 74342

African (AFR) AF: 0.144 AC: 5979 AN: 41500

American (AMR) AF: 0.270 AC: 4128 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2045 AN: 5162

South Asian (SAS) AF: 0.334 AC: 1605 AN: 4802

European-Finnish (FIN) AF: 0.310 AC: 3270 AN: 10564

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19552 AN: 67972

Other (OTH) AF: 0.278 AC: 586 AN: 2108

Alfa AF: 0.148 Hom.: 289

Bravo AF: 0.247

Asia WGS AF: 0.358 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.74
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs1152731; hg19: chr1-10914807;