rs17831941

chr2-49257317-A-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, non coding transcript 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: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634588.1	n.493-150885A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000635306.1	n.408-38689T>C		intron_variant, non_coding_transcript_variant		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;