chr4-175628973-A-T

Variant names:

• chr4-175628973-A-T
• rs2333244

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 0.358 in 151,932 control chromosomes in the GnomAD database, including 10,474 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 0.36 (10474 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.358 AC: 54355 AN: 151812 Hom.: 10461 Cov.: 31

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.358 AC: 54390 AN: 151932 Hom.: 10474 Cov.: 31 AF XY: 0.364 AC XY: 27046 AN XY: 74238

African (AFR) AF: 0.217 AC: 9001 AN: 41436

American (AMR) AF: 0.475 AC: 7251 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2637 AN: 5154

South Asian (SAS) AF: 0.393 AC: 1895 AN: 4822

European-Finnish (FIN) AF: 0.451 AC: 4754 AN: 10538

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26386 AN: 67928

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.365 Hom.: 1299

Bravo AF: 0.355

Asia WGS AF: 0.428 AC: 1489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	1.7
DANN	Benign	0.58
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2333244; hg19: chr4-176550124;