rs731069

Variant names:

• chr4-10150807-A-C
• rs731069

Your query was ambiguous. Multiple possible variants found:

• chr4-10150807-A-C
• chr4-10150807-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 0.427 in 151,722 control chromosomes in the GnomAD database, including 14,227 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 0.43 (14227 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 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: 0.427 AC: 64753 AN: 151602 Hom.: 14211 Cov.: 31

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.427 AC: 64810 AN: 151722 Hom.: 14227 Cov.: 31 AF XY: 0.422 AC XY: 31307 AN XY: 74174

African (AFR) AF: 0.395 AC: 16317 AN: 41304

American (AMR) AF: 0.449 AC: 6850 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3468

East Asian (EAS) AF: 0.167 AC: 859 AN: 5146

South Asian (SAS) AF: 0.337 AC: 1622 AN: 4806

European-Finnish (FIN) AF: 0.408 AC: 4299 AN: 10542

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31237 AN: 67904

Other (OTH) AF: 0.454 AC: 950 AN: 2094

Alfa AF: 0.384 Hom.: 2335

Bravo AF: 0.433

Asia WGS AF: 0.269 AC: 935 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.67
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs731069; hg19: chr4-10152431;