5-39676175-T-C

Position:

• chr5-39676175-T-C

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 0.877 in 152,100 control chromosomes in the GnomAD database, including 59,316 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 0.88 (59316 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133368 AN: 151982 Hom.: 59279 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.952

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.877 AC: 133458 AN: 152100 Hom.: 59316 Cov.: 31 AF XY: 0.873 AC XY: 64931 AN XY: 74344

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.823

Gnomad4 ASJ AF: 0.945

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.936

Gnomad4 NFE AF: 0.952

Gnomad4 OTH AF: 0.892

Alfa AF: 0.893 Hom.: 12005

Bravo AF: 0.863

Asia WGS AF: 0.745 AC: 2590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.31
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4957217; hg19: chr5-39676277;