ENST00000687336.1:n.203C>T

Variant names:

• chr2-61764103-G-A
• rs1186868
• ENST00000687336.2:n.597C>T

Variant summary

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

The ENST00000687336.2(ENSG00000289410):​n.597C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 152,236 control chromosomes in the GnomAD database, including 429 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 0.069 (429 hom., cov: 32)
• Consequence: ENSG00000289410 ENST00000687336.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 4 publications found

Genes affected

ENSG00000289410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687336.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289410	ENST00000687336.2		n.597C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289410	ENST00000689428.1		n.99C>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000289855	ENST00000701106.2		n.211G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10458 AN: 152118 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.0489

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0511

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0692

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0687 AC: 10461 AN: 152236 Hom.: 429 Cov.: 32 AF XY: 0.0662 AC XY: 4931 AN XY: 74432

African (AFR) AF: 0.0893 AC: 3711 AN: 41544

American (AMR) AF: 0.0489 AC: 747 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4828

European-Finnish (FIN) AF: 0.0511 AC: 542 AN: 10600

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0692 AC: 4704 AN: 68004

Other (OTH) AF: 0.0610 AC: 129 AN: 2114

Alfa AF: 0.0591 Hom.: 201

Bravo AF: 0.0711

Asia WGS AF: 0.0140 AC: 47 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.0
DANN	Benign	0.94
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1186868; hg19: chr2-61991238;