rs261119

Variant names:

• chr5-4365355-G-A
• rs261119

Your query was ambiguous. Multiple possible variants found:

• chr5-4365355-G-A
• chr5-4365355-G-C
• chr5-4365355-G-T

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 0.456 in 151,974 control chromosomes in the GnomAD database, including 16,351 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 0.46 (16351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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: 0.456 AC: 69236 AN: 151856 Hom.: 16354 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.456 AC: 69246 AN: 151974 Hom.: 16351 Cov.: 32 AF XY: 0.457 AC XY: 33904 AN XY: 74268

African (AFR) AF: 0.366 AC: 15141 AN: 41424

American (AMR) AF: 0.368 AC: 5615 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1584 AN: 3472

East Asian (EAS) AF: 0.671 AC: 3457 AN: 5152

South Asian (SAS) AF: 0.456 AC: 2198 AN: 4820

European-Finnish (FIN) AF: 0.529 AC: 5588 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34259 AN: 67950

Other (OTH) AF: 0.447 AC: 941 AN: 2106

Alfa AF: 0.479 Hom.: 7356

Bravo AF: 0.440

Asia WGS AF: 0.533 AC: 1852 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.076
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs261119; hg19: chr5-4365468;