rs17831941

Variant names:

• chr2-49257317-A-G
• rs17831941
• ENST00000634588.1:n.493-150885A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634588.1(ENSG00000282890):​n.493-150885A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,262 control chromosomes in the GnomAD database, including 445 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 0.068 (445 hom., cov: 32)
• Consequence: ENSG00000282890 ENST00000634588.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

ENSG00000282890 (HGNC:58158):

ENSG00000282998 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0959 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
ENSG00000282890	ENST00000634588.1	n.493-150885A>G		intron_variant	Intron 2 of 4	5
ENSG00000282998	ENST00000635306.1	n.408-38689T>C		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10411 AN: 152144 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.0846

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

GnomAD4 genome AF: 0.0684 AC: 10418 AN: 152262 Hom.: 445 Cov.: 32 AF XY: 0.0674 AC XY: 5016 AN XY: 74432

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.0989

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0387

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.0979

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0798 Hom.: 100

Bravo AF: 0.0655

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17831941; hg19: chr2-49484456;