4-73991991-A-G

Variant names:

• chr4-73991991-A-G
• rs2472649

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 0.644 in 152,142 control chromosomes in the GnomAD database, including 37,594 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 0.64 (37594 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 52 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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: 0.645 AC: 98054 AN: 152024 Hom.: 37600 Cov.: 33

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.644 AC: 98045 AN: 152142 Hom.: 37594 Cov.: 33 AF XY: 0.650 AC XY: 48325 AN XY: 74370

African (AFR) AF: 0.199 AC: 8271 AN: 41512

American (AMR) AF: 0.733 AC: 11191 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2700 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4312 AN: 5180

South Asian (SAS) AF: 0.753 AC: 3630 AN: 4822

European-Finnish (FIN) AF: 0.849 AC: 8982 AN: 10580

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.831 AC: 56526 AN: 67990

Other (OTH) AF: 0.673 AC: 1421 AN: 2110

Alfa AF: 0.766 Hom.: 159611

Bravo AF: 0.612

Asia WGS AF: 0.694 AC: 2409 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs2472649; hg19: chr4-74857708;