5-3741161-A-T

Position:

• chr5-3741161-A-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 0.376 in 152,170 control chromosomes in the GnomAD database, including 11,855 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 0.38 (11855 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.376 AC: 57215 AN: 152052 Hom.: 11848 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.376 AC: 57240 AN: 152170 Hom.: 11855 Cov.: 33 AF XY: 0.380 AC XY: 28242 AN XY: 74388

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.420

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.392

Alfa AF: 0.405 Hom.: 1636

Bravo AF: 0.366

Asia WGS AF: 0.430 AC: 1493 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924674; hg19: chr5-3741275;