5-26356195-G-C

Position:

• chr5-26356195-G-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 0.134 in 147,362 control chromosomes in the GnomAD database, including 1,615 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 0.13 (1615 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26356195G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.134 AC: 19790 AN: 147290 Hom.: 1617 Cov.: 30

Gnomad AFR AF: 0.0345

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.134 AC: 19789 AN: 147362 Hom.: 1615 Cov.: 30 AF XY: 0.135 AC XY: 9696 AN XY: 71680

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0818 Hom.: 132

Bravo AF: 0.127

Asia WGS AF: 0.170 AC: 590 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.31
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1121737; hg19: chr5-26356304;