5-175184337-T-C

Variant names:

• chr5-175184337-T-C
• rs4336372

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 0.574 in 151,968 control chromosomes in the GnomAD database, including 25,973 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 0.57 (25973 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.255
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87232 AN: 151850 Hom.: 25957 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.574 AC: 87291 AN: 151968 Hom.: 25973 Cov.: 31 AF XY: 0.575 AC XY: 42711 AN XY: 74290

African (AFR) AF: 0.437 AC: 18089 AN: 41420

American (AMR) AF: 0.485 AC: 7412 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2147 AN: 3464

East Asian (EAS) AF: 0.558 AC: 2880 AN: 5162

South Asian (SAS) AF: 0.628 AC: 3020 AN: 4810

European-Finnish (FIN) AF: 0.679 AC: 7182 AN: 10570

Middle Eastern (MID) AF: 0.586 AC: 171 AN: 292

European-Non Finnish (NFE) AF: 0.657 AC: 44658 AN: 67954

Other (OTH) AF: 0.559 AC: 1180 AN: 2110

Alfa AF: 0.602 Hom.: 46680

Bravo AF: 0.552

Asia WGS AF: 0.531 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs4336372; hg19: chr5-174611340; COSMIC: COSV60235874;