5-26225726-G-C

Variant names:

• chr5-26225726-G-C
• rs1788

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 0.662 in 151,382 control chromosomes in the GnomAD database, including 33,195 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 0.66 (33195 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.728 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: 0.662 AC: 100080 AN: 151264 Hom.: 33166 Cov.: 30

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.662 AC: 100163 AN: 151382 Hom.: 33195 Cov.: 30 AF XY: 0.661 AC XY: 48873 AN XY: 73958

African (AFR) AF: 0.657 AC: 27106 AN: 41254

American (AMR) AF: 0.740 AC: 11277 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2428 AN: 3462

East Asian (EAS) AF: 0.700 AC: 3553 AN: 5076

South Asian (SAS) AF: 0.635 AC: 3044 AN: 4790

European-Finnish (FIN) AF: 0.590 AC: 6165 AN: 10448

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44309 AN: 67806

Other (OTH) AF: 0.686 AC: 1438 AN: 2096

Alfa AF: 0.560 Hom.: 1599

Bravo AF: 0.674

Asia WGS AF: 0.677 AC: 2354 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	0.77
DANN	Benign	0.39
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1788; hg19: chr5-26225835;