5-138469963-G-T

Variant names:

• chr5-138469963-G-T
• rs11741807

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 0.545 in 152,104 control chromosomes in the GnomAD database, including 23,473 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 0.55 (23473 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 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: 0.545 AC: 82833 AN: 151984 Hom.: 23440 Cov.: 33

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.545 AC: 82920 AN: 152104 Hom.: 23473 Cov.: 33 AF XY: 0.543 AC XY: 40330 AN XY: 74338

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.548

Alfa AF: 0.578 Hom.: 33100

Bravo AF: 0.535

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11741807; hg19: chr5-137805652;