5-136003151-C-T

Variant names:

• chr5-136003151-C-T
• rs30747

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 0.928 in 152,286 control chromosomes in the GnomAD database, including 65,751 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 0.93 (65751 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 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: 0.928 AC: 141234 AN: 152168 Hom.: 65708 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.904

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.921

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

GnomAD4 genome AF: 0.928 AC: 141334 AN: 152286 Hom.: 65751 Cov.: 32 AF XY: 0.926 AC XY: 68995 AN XY: 74476

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.904

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.922

Alfa AF: 0.931 Hom.: 69979

Bravo AF: 0.925

Asia WGS AF: 0.820 AC: 2849 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30747; hg19: chr5-135338840;