5-39676175-T-C

Variant names:

• chr5-39676175-T-C
• rs4957217

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;