5-4369774-G-T

Variant names:

• chr5-4369774-G-T
• rs261125

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.46 in 152,038 control chromosomes in the GnomAD database, including 16,592 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 0.46 (16592 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.654 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: 0.460 AC: 69935 AN: 151920 Hom.: 16594 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.460 AC: 69952 AN: 152038 Hom.: 16592 Cov.: 33 AF XY: 0.461 AC XY: 34253 AN XY: 74344

African (AFR) AF: 0.381 AC: 15821 AN: 41472

American (AMR) AF: 0.369 AC: 5636 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1581 AN: 3468

East Asian (EAS) AF: 0.673 AC: 3469 AN: 5156

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4820

European-Finnish (FIN) AF: 0.528 AC: 5575 AN: 10566

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34264 AN: 67968

Other (OTH) AF: 0.448 AC: 944 AN: 2108

Alfa AF: 0.480 Hom.: 48764

Bravo AF: 0.445

Asia WGS AF: 0.537 AC: 1865 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.36
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs261125; hg19: chr5-4369887;