5-26077906-A-G

Variant names:

• chr5-26077906-A-G
• rs1360315

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 0.964 in 152,102 control chromosomes in the GnomAD database, including 70,887 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 0.96 (70887 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 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: 0.965 AC: 146598 AN: 151984 Hom.: 70843 Cov.: 31

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.986

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.999

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.964 AC: 146698 AN: 152102 Hom.: 70887 Cov.: 31 AF XY: 0.964 AC XY: 71684 AN XY: 74374

African (AFR) AF: 0.900 AC: 37344 AN: 41482

American (AMR) AF: 0.986 AC: 15025 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3415 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5145 AN: 5156

South Asian (SAS) AF: 0.892 AC: 4305 AN: 4828

European-Finnish (FIN) AF: 0.999 AC: 10606 AN: 10614

Middle Eastern (MID) AF: 0.962 AC: 279 AN: 290

European-Non Finnish (NFE) AF: 0.995 AC: 67627 AN: 67998

Other (OTH) AF: 0.970 AC: 2045 AN: 2108

Alfa AF: 0.974 Hom.: 10905

Bravo AF: 0.963

Asia WGS AF: 0.913 AC: 3173 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.63
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1360315; hg19: chr5-26078015;