rs2708092

Variant names:

• chr12-121088083-G-A
• rs2708092
• ENST00000837362.1:n.258C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-121088083-G-A
• chr12-121088083-G-C

Variant summary

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

The ENST00000837362.1(ENSG00000308932):​n.258C>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 0.733 in 152,090 control chromosomes in the GnomAD database, including 41,682 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 0.73 (41682 hom., cov: 32)
• Consequence: ENSG00000308932 ENST00000837362.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 5 publications found

Genes affected

ENSG00000308932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378258	XR_007063492.1	n.4913C>T		non_coding_transcript_exon_variant	Exon 1 of 4
LOC105378258	XR_945451.4	n.4913C>T		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308932	ENST00000837362.1	n.258C>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000308932	ENST00000837363.1	n.762C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308932	ENST00000837364.1	n.207C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000308947	ENST00000837477.1	n.540+668G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111484 AN: 151972 Hom.: 41677 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.470

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.733 AC: 111539 AN: 152090 Hom.: 41682 Cov.: 32 AF XY: 0.734 AC XY: 54566 AN XY: 74354

African (AFR) AF: 0.607 AC: 25167 AN: 41450

American (AMR) AF: 0.784 AC: 11998 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2585 AN: 3466

East Asian (EAS) AF: 0.471 AC: 2432 AN: 5168

South Asian (SAS) AF: 0.808 AC: 3892 AN: 4814

European-Finnish (FIN) AF: 0.825 AC: 8742 AN: 10600

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54278 AN: 67984

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.780 Hom.: 58150

Bravo AF: 0.721

Asia WGS AF: 0.665 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.27
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2708092; hg19: chr12-121525886;