3-89485227-T-C

Variant names:

• chr3-89485227-T-C
• rs7632427

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 0.431 in 147,158 control chromosomes in the GnomAD database, including 14,035 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 (14035 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515
• Publications: 35 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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: 0.431 AC: 63322 AN: 147054 Hom.: 14009 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.431 AC: 63381 AN: 147158 Hom.: 14035 Cov.: 31 AF XY: 0.427 AC XY: 30780 AN XY: 72016

African (AFR) AF: 0.574 AC: 21287 AN: 37104

American (AMR) AF: 0.359 AC: 5384 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3464

East Asian (EAS) AF: 0.177 AC: 910 AN: 5138

South Asian (SAS) AF: 0.248 AC: 1193 AN: 4816

European-Finnish (FIN) AF: 0.504 AC: 5309 AN: 10524

Middle Eastern (MID) AF: 0.330 AC: 95 AN: 288

European-Non Finnish (NFE) AF: 0.396 AC: 26889 AN: 67850

Other (OTH) AF: 0.409 AC: 842 AN: 2058

Alfa AF: 0.395 Hom.: 22255

Bravo AF: 0.435

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.37
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs7632427; hg19: chr3-89534377;