chr5-90324283-A-G

Variant names:

• chr5-90324283-A-G
• rs2972956

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 0.932 in 152,270 control chromosomes in the GnomAD database, including 66,283 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 0.93 (66283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141818 AN: 152152 Hom.: 66212 Cov.: 32

Gnomad AFR AF: 0.982

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.932 AC: 141947 AN: 152270 Hom.: 66283 Cov.: 32 AF XY: 0.935 AC XY: 69579 AN XY: 74452

African (AFR) AF: 0.982 AC: 40802 AN: 41550

American (AMR) AF: 0.933 AC: 14278 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3033 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5172 AN: 5180

South Asian (SAS) AF: 0.924 AC: 4457 AN: 4826

European-Finnish (FIN) AF: 0.963 AC: 10212 AN: 10608

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60922 AN: 68018

Other (OTH) AF: 0.936 AC: 1978 AN: 2114

Alfa AF: 0.906 Hom.: 31066

Bravo AF: 0.935

Asia WGS AF: 0.967 AC: 3365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.25
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2972956; hg19: chr5-89620100;