rs2696161

chr2-49390359-A-C

Variant summary

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

The ENST00000634588.1(ENSG00000282890):n.493-17843A>C 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 0.0821 in 152,054 control chromosomes in the GnomAD database, including 562 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 0.082 (562 hom., cov: 32)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 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.493-17843A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000635306.1	n.300+36173T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000634539.1	n.102+36173T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0822 AC: 12484 AN: 151938 Hom.: 562 Cov.: 32

Gnomad AFR AF: 0.0494

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0362

Gnomad FIN AF: 0.0840

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.0821 AC: 12479 AN: 152054 Hom.: 562 Cov.: 32 AF XY: 0.0781 AC XY: 5809 AN XY: 74346

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.0546

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.0840

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.0977 Hom.: 137

Bravo AF: 0.0768

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.9
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2696161; hg19: chr2-49617498;