rs2939244

Variant names:

• chr5-91778169-T-A
• rs2939244
• ENST00000651690.1:n.459-5688T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-91778169-T-A
• chr5-91778169-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651690.1(ENSG00000286121):​n.459-5688T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 151,994 control chromosomes in the GnomAD database, including 37,522 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 0.70 (37522 hom., cov: 32)
• Consequence: ENSG00000286121 ENST00000651690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.53
• Publications: 9 publications found

Genes affected

ENSG00000286121 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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
ENSG00000286121	ENST00000651690.1	n.459-5688T>A		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105955 AN: 151876 Hom.: 37470 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.698 AC: 106062 AN: 151994 Hom.: 37522 Cov.: 32 AF XY: 0.695 AC XY: 51613 AN XY: 74288

African (AFR) AF: 0.807 AC: 33482 AN: 41508

American (AMR) AF: 0.682 AC: 10402 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2340 AN: 5156

South Asian (SAS) AF: 0.599 AC: 2890 AN: 4822

European-Finnish (FIN) AF: 0.693 AC: 7315 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45167 AN: 67916

Other (OTH) AF: 0.677 AC: 1432 AN: 2114

Alfa AF: 0.598 Hom.: 1856

Bravo AF: 0.702

Asia WGS AF: 0.608 AC: 2108 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.64
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs2939244; hg19: chr5-91073986;