5-135994226-T-G

Position:

• chr5-135994226-T-G

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 0.322 in 152,148 control chromosomes in the GnomAD database, including 8,641 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 0.32 (8641 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48837 AN: 152030 Hom.: 8608 Cov.: 33

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.377

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.322 AC: 48928 AN: 152148 Hom.: 8641 Cov.: 33 AF XY: 0.321 AC XY: 23894 AN XY: 74388

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.317

Alfa AF: 0.274 Hom.: 4676

Bravo AF: 0.330

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	17
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12520800; hg19: chr5-135329915;