chr5-136002569-T-C

Position:

• chr5-136002569-T-C

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 0.592 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.553

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.580

Alfa AF: 0.582 Hom.: 32988

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs30746; hg19: chr5-135338258;