4-111477457-T-G

Variant names:

• chr4-111477457-T-G
• rs2654735

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 0.372 in 151,302 control chromosomes in the GnomAD database, including 11,107 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 0.37 (11107 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.424 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: 0.372 AC: 56226 AN: 151186 Hom.: 11106 Cov.: 31

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.372 AC: 56247 AN: 151302 Hom.: 11107 Cov.: 31 AF XY: 0.372 AC XY: 27467 AN XY: 73928

African (AFR) AF: 0.286 AC: 11810 AN: 41350

American (AMR) AF: 0.355 AC: 5388 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3464

East Asian (EAS) AF: 0.168 AC: 867 AN: 5154

South Asian (SAS) AF: 0.340 AC: 1635 AN: 4804

European-Finnish (FIN) AF: 0.484 AC: 5010 AN: 10358

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 28968 AN: 67702

Other (OTH) AF: 0.349 AC: 728 AN: 2088

Alfa AF: 0.405 Hom.: 52844

Bravo AF: 0.360

Asia WGS AF: 0.288 AC: 994 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.99
DANN	Benign	0.73
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs2654735; hg19: chr4-112398613;