rs2696161

Variant names:

• chr2-49390359-A-C
• rs2696161
• ENST00000634539.1:n.102+36173T>G

Variant summary

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

The ENST00000634539.1(ENSG00000282998):​n.102+36173T>G variant causes a intron 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: ENSG00000282998 ENST00000634539.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 0 publications found

Genes affected

ENSG00000282998 (HGNC:):

ENSG00000282890 (HGNC:58158):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634539.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282998	ENST00000634539.1	TSL:5	n.102+36173T>G		intron	N/A
	ENSG00000282890	ENST00000634588.1	TSL:5	n.493-17843A>C		intron	N/A
	ENSG00000282998	ENST00000635306.2	TSL:5	n.300+36173T>G		intron	N/A

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

African (AFR) AF: 0.0493 AC: 2049 AN: 41532

American (AMR) AF: 0.0546 AC: 832 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 411 AN: 3466

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0358 AC: 173 AN: 4826

European-Finnish (FIN) AF: 0.0840 AC: 891 AN: 10606

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7831 AN: 67880

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

Alfa AF: 0.0967 Hom.: 137

Bravo AF: 0.0768

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.42
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs2696161; hg19: chr2-49617498;