chr5-175469183-G-T

Variant names:

• chr5-175469183-G-T
• rs2644645

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 0.459 in 151,932 control chromosomes in the GnomAD database, including 16,285 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 0.46 (16285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.468 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: 0.459 AC: 69735 AN: 151812 Hom.: 16263 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.459 AC: 69810 AN: 151932 Hom.: 16285 Cov.: 32 AF XY: 0.458 AC XY: 34021 AN XY: 74258

African (AFR) AF: 0.474 AC: 19625 AN: 41418

American (AMR) AF: 0.464 AC: 7089 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1978 AN: 5150

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4814

European-Finnish (FIN) AF: 0.481 AC: 5073 AN: 10548

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31426 AN: 67932

Other (OTH) AF: 0.446 AC: 944 AN: 2116

Alfa AF: 0.439 Hom.: 10508

Bravo AF: 0.460

Asia WGS AF: 0.351 AC: 1218 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.61
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2644645; hg19: chr5-174896186; COSMIC: COSV60236942;