5-136002569-T-C

Variant names:

• chr5-136002569-T-C
• rs30746

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 0.592 in 152,124 control chromosomes in the GnomAD database, including 26,614 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 0.59 (26614 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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: 0.592 AC: 89913 AN: 152006 Hom.: 26590 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.592 AC: 89986 AN: 152124 Hom.: 26614 Cov.: 33 AF XY: 0.590 AC XY: 43884 AN XY: 74380

African (AFR) AF: 0.579 AC: 24024 AN: 41488

American (AMR) AF: 0.601 AC: 9192 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3468

East Asian (EAS) AF: 0.650 AC: 3366 AN: 5176

South Asian (SAS) AF: 0.553 AC: 2665 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6398 AN: 10590

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40265 AN: 67972

Other (OTH) AF: 0.580 AC: 1227 AN: 2114

Alfa AF: 0.587 Hom.: 50170

Bravo AF: 0.594

Asia WGS AF: 0.629 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.30
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs30746; hg19: chr5-135338258;