chr5-135957019-G-A

Position:

• chr5-135957019-G-A

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 0.792 in 152,180 control chromosomes in the GnomAD database, including 48,431 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 0.79 (48431 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.135957019G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120344 AN: 152062 Hom.: 48364 Cov.: 32

Gnomad AFR AF: 0.943

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.755

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.792 AC: 120466 AN: 152180 Hom.: 48431 Cov.: 32 AF XY: 0.793 AC XY: 58988 AN XY: 74400

Gnomad4 AFR AF: 0.943

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.813

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.763

Alfa AF: 0.752 Hom.: 5092

Bravo AF: 0.799

Asia WGS AF: 0.803 AC: 2791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248166; hg19: chr5-135292708;