5-175184337-T-C

Variant names:

• chr5-175184337-T-C
• rs4336372

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.620

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.559

Alfa AF: 0.632 Hom.: 29176

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

Splicing

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

Publications

LitVar

Other links and lift over

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