5-173852839-C-T

Position:

• chr5-173852839-C-T

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 0.583 in 151,922 control chromosomes in the GnomAD database, including 26,304 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 0.58 (26304 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88533 AN: 151804 Hom.: 26280 Cov.: 31

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.583 AC: 88601 AN: 151922 Hom.: 26304 Cov.: 31 AF XY: 0.577 AC XY: 42827 AN XY: 74190

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.624

Alfa AF: 0.570 Hom.: 56177

Bravo AF: 0.581

Asia WGS AF: 0.561 AC: 1951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs359457; hg19: chr5-173279842; COSMIC: COSV60233946;