4-81233128-A-T

Variant names:

• chr4-81233128-A-T
• rs1662845

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 0.581 in 151,968 control chromosomes in the GnomAD database, including 28,842 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 0.58 (28842 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88227 AN: 151850 Hom.: 28781 Cov.: 31

Gnomad AFR AF: 0.898

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.581 AC: 88345 AN: 151968 Hom.: 28842 Cov.: 31 AF XY: 0.578 AC XY: 42881 AN XY: 74244

African (AFR) AF: 0.898 AC: 37258 AN: 41494

American (AMR) AF: 0.573 AC: 8739 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1927 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2380 AN: 5152

South Asian (SAS) AF: 0.405 AC: 1949 AN: 4812

European-Finnish (FIN) AF: 0.447 AC: 4703 AN: 10524

Middle Eastern (MID) AF: 0.497 AC: 143 AN: 288

European-Non Finnish (NFE) AF: 0.437 AC: 29686 AN: 67954

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.526 Hom.: 2889

Bravo AF: 0.610

Asia WGS AF: 0.472 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.74
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs1662845; hg19: chr4-82154282;