rs1455474

Variant names:

• chr8-135365743-G-A
• rs1455474

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 0.507 in 151,940 control chromosomes in the GnomAD database, including 21,850 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 0.51 (21850 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.507 AC: 77004 AN: 151822 Hom.: 21810 Cov.: 31

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.507 AC: 77093 AN: 151940 Hom.: 21850 Cov.: 31 AF XY: 0.500 AC XY: 37127 AN XY: 74240

African (AFR) AF: 0.785 AC: 32552 AN: 41448

American (AMR) AF: 0.436 AC: 6651 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3468

East Asian (EAS) AF: 0.499 AC: 2558 AN: 5128

South Asian (SAS) AF: 0.403 AC: 1942 AN: 4814

European-Finnish (FIN) AF: 0.305 AC: 3219 AN: 10566

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26956 AN: 67944

Other (OTH) AF: 0.500 AC: 1056 AN: 2110

Alfa AF: 0.441 Hom.: 16574

Bravo AF: 0.533

Asia WGS AF: 0.453 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.43
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1455474; hg19: chr8-136377986;