rs2120991

Variant names:

• chr12-53876444-C-A
• rs2120991
• ENST00000819907.1:n.41G>T

Variant summary

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

The ENST00000819907.1(ENSG00000306638):​n.41G>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 0.272 in 152,058 control chromosomes in the GnomAD database, including 6,846 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 0.27 (6846 hom., cov: 32)
• Consequence: ENSG00000306638 ENST00000819907.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 15 publications found

Genes affected

ENSG00000306638 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819907.1. 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
	LOC105378250	NR_189097.1		n.399-19753C>A		intron	N/A
	LOC105378250	NR_189098.1		n.590+1196C>A		intron	N/A
	LOC105378250	NR_189099.1		n.591+15566C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306638	ENST00000819907.1		n.41G>T		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000286069	ENST00000652339.1		n.509+15566C>A		intron	N/A
	ENSG00000286069	ENST00000654713.2		n.318-19753C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41335 AN: 151938 Hom.: 6849 Cov.: 32

Gnomad AFR AF: 0.0908

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.272 AC: 41325 AN: 152058 Hom.: 6846 Cov.: 32 AF XY: 0.267 AC XY: 19835 AN XY: 74302

African (AFR) AF: 0.0905 AC: 3758 AN: 41530

American (AMR) AF: 0.217 AC: 3315 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1382 AN: 3464

East Asian (EAS) AF: 0.157 AC: 816 AN: 5186

South Asian (SAS) AF: 0.304 AC: 1466 AN: 4822

European-Finnish (FIN) AF: 0.314 AC: 3315 AN: 10548

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26266 AN: 67906

Other (OTH) AF: 0.269 AC: 568 AN: 2114

Alfa AF: 0.332 Hom.: 23593

Bravo AF: 0.253

Asia WGS AF: 0.232 AC: 810 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.33
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2120991;

hg19: chr12-54270228;