5-26356195-G-C

Variant names:

• chr5-26356195-G-C
• rs1121737

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 0.134 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0344 AC: 1383 AN: 40208

American (AMR) AF: 0.144 AC: 2134 AN: 14804

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 718 AN: 3442

East Asian (EAS) AF: 0.195 AC: 986 AN: 5062

South Asian (SAS) AF: 0.173 AC: 807 AN: 4656

European-Finnish (FIN) AF: 0.159 AC: 1475 AN: 9272

Middle Eastern (MID) AF: 0.106 AC: 30 AN: 284

European-Non Finnish (NFE) AF: 0.178 AC: 11856 AN: 66714

Other (OTH) AF: 0.131 AC: 266 AN: 2034

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1121737; hg19: chr5-26356304;