5-25898911-T-C

Variant names:

• chr5-25898911-T-C
• rs1896731

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 0.385 in 151,956 control chromosomes in the GnomAD database, including 11,532 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 0.39 (11532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.385 AC: 58452 AN: 151838 Hom.: 11517 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.385 AC: 58515 AN: 151956 Hom.: 11532 Cov.: 32 AF XY: 0.389 AC XY: 28856 AN XY: 74262

African (AFR) AF: 0.413 AC: 17123 AN: 41434

American (AMR) AF: 0.400 AC: 6104 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.591 AC: 3041 AN: 5148

South Asian (SAS) AF: 0.448 AC: 2160 AN: 4822

European-Finnish (FIN) AF: 0.363 AC: 3832 AN: 10550

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24050 AN: 67950

Other (OTH) AF: 0.376 AC: 793 AN: 2108

Alfa AF: 0.362 Hom.: 43115

Bravo AF: 0.385

Asia WGS AF: 0.503 AC: 1742 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.80
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs1896731; hg19: chr5-25899020;