5-105961828-T-G

Variant names:

• chr5-105961828-T-G
• rs13189969

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 0.569 in 151,862 control chromosomes in the GnomAD database, including 25,385 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 0.57 (25385 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.569 AC: 86306 AN: 151744 Hom.: 25354 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.676

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.624

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.569 AC: 86399 AN: 151862 Hom.: 25385 Cov.: 31 AF XY: 0.579 AC XY: 42916 AN XY: 74178

African (AFR) AF: 0.483 AC: 19997 AN: 41400

American (AMR) AF: 0.677 AC: 10317 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2086 AN: 3468

East Asian (EAS) AF: 0.962 AC: 4972 AN: 5168

South Asian (SAS) AF: 0.729 AC: 3507 AN: 4808

European-Finnish (FIN) AF: 0.544 AC: 5721 AN: 10522

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.559 AC: 37977 AN: 67940

Other (OTH) AF: 0.589 AC: 1245 AN: 2114

Alfa AF: 0.559 Hom.: 35470

Bravo AF: 0.572

Asia WGS AF: 0.828 AC: 2875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.77
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs13189969; hg19: chr5-105297529;