4-155585717-T-C

Variant names:

• chr4-155585717-T-C
• rs716428

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 0.525 in 152,086 control chromosomes in the GnomAD database, including 21,406 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 0.52 (21406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570

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 (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.525 AC: 79769 AN: 151968 Hom.: 21401 Cov.: 32

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.525 AC: 79817 AN: 152086 Hom.: 21406 Cov.: 32 AF XY: 0.536 AC XY: 39830 AN XY: 74338

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.525

Alfa AF: 0.527 Hom.: 4603

Bravo AF: 0.510

Asia WGS AF: 0.676 AC: 2347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716428; hg19: chr4-156506869;