7-81372428-G-A

Variant names:

• chr7-81372428-G-A
• rs2189915

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 151,650 control chromosomes in the GnomAD database, including 5,735 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 (5735 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.335 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: 0.253 AC: 38348 AN: 151536 Hom.: 5739 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.253 AC: 38337 AN: 151650 Hom.: 5735 Cov.: 31 AF XY: 0.254 AC XY: 18790 AN XY: 74078

African (AFR) AF: 0.109 AC: 4510 AN: 41348

American (AMR) AF: 0.238 AC: 3619 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 753 AN: 3462

East Asian (EAS) AF: 0.115 AC: 587 AN: 5124

South Asian (SAS) AF: 0.210 AC: 1006 AN: 4792

European-Finnish (FIN) AF: 0.360 AC: 3783 AN: 10518

Middle Eastern (MID) AF: 0.234 AC: 68 AN: 290

European-Non Finnish (NFE) AF: 0.338 AC: 22965 AN: 67862

Other (OTH) AF: 0.282 AC: 594 AN: 2110

Alfa AF: 0.305 Hom.: 12819

Bravo AF: 0.236

Asia WGS AF: 0.166 AC: 577 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.98
DANN	Benign	0.74
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs2189915; hg19: chr7-81001744;