rs2972994

Variant names:

• chr5-42756398-G-A
• rs2972994

Your query was ambiguous. Multiple possible variants found:

• chr5-42756398-G-A
• chr5-42756398-G-C

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 0.446 in 151,936 control chromosomes in the GnomAD database, including 15,330 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 0.45 (15330 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 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: 0.447 AC: 67822 AN: 151818 Hom.: 15343 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.446 AC: 67817 AN: 151936 Hom.: 15330 Cov.: 31 AF XY: 0.447 AC XY: 33173 AN XY: 74262

African (AFR) AF: 0.441 AC: 18269 AN: 41432

American (AMR) AF: 0.401 AC: 6124 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3470

East Asian (EAS) AF: 0.581 AC: 3003 AN: 5166

South Asian (SAS) AF: 0.478 AC: 2296 AN: 4804

European-Finnish (FIN) AF: 0.363 AC: 3828 AN: 10542

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31283 AN: 67952

Other (OTH) AF: 0.450 AC: 945 AN: 2102

Alfa AF: 0.438 Hom.: 1833

Bravo AF: 0.449

Asia WGS AF: 0.536 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.64
PhyloP100		0.21
PromoterAI		-0.024	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2972994; hg19: chr5-42756500;