5-26864905-A-G

Variant names:

• chr5-26864905-A-G
• rs2035282

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 0.609 in 151,620 control chromosomes in the GnomAD database, including 28,856 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 0.61 (28856 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.609 AC: 92217 AN: 151504 Hom.: 28814 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.781

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.609 AC: 92320 AN: 151620 Hom.: 28856 Cov.: 31 AF XY: 0.613 AC XY: 45422 AN XY: 74080

African (AFR) AF: 0.688 AC: 28475 AN: 41398

American (AMR) AF: 0.703 AC: 10681 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3468

East Asian (EAS) AF: 0.828 AC: 4229 AN: 5108

South Asian (SAS) AF: 0.792 AC: 3821 AN: 4822

European-Finnish (FIN) AF: 0.469 AC: 4930 AN: 10520

Middle Eastern (MID) AF: 0.771 AC: 222 AN: 288

European-Non Finnish (NFE) AF: 0.535 AC: 36259 AN: 67800

Other (OTH) AF: 0.649 AC: 1370 AN: 2112

Alfa AF: 0.575 Hom.: 3309

Bravo AF: 0.629

Asia WGS AF: 0.812 AC: 2802 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.45
DANN	Benign	0.25
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2035282; hg19: chr5-26865014;