2-172212112-A-G

Variant names:

• chr2-172212112-A-G
• rs12614495
• ENST00000735536.1:n.386T>C

Variant summary

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

The ENST00000735536.1(ENSG00000296020):​n.386T>C 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 0.723 in 152,024 control chromosomes in the GnomAD database, including 41,589 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 0.72 (41589 hom., cov: 31)
• Consequence: ENSG00000296020 ENST00000735536.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 4 publications found

Genes affected

ENSG00000296020 (HGNC:):

DLX2-DT (HGNC:50638): (DLX2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735536.1. 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
	ENSG00000296020	ENST00000735536.1		n.386T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000296020	ENST00000735537.1		n.307T>C		non_coding_transcript_exon	Exon 2 of 2
	DLX2-DT	ENST00000662340.1		n.212+67136A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109882 AN: 151906 Hom.: 41569 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.723 AC: 109942 AN: 152024 Hom.: 41589 Cov.: 31 AF XY: 0.731 AC XY: 54279 AN XY: 74302

African (AFR) AF: 0.482 AC: 19982 AN: 41428

American (AMR) AF: 0.754 AC: 11522 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2673 AN: 3472

East Asian (EAS) AF: 0.795 AC: 4092 AN: 5150

South Asian (SAS) AF: 0.775 AC: 3736 AN: 4820

European-Finnish (FIN) AF: 0.920 AC: 9733 AN: 10576

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.821 AC: 55813 AN: 67994

Other (OTH) AF: 0.717 AC: 1509 AN: 2104

Alfa AF: 0.753 Hom.: 7496

Bravo AF: 0.697

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.34
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs12614495; hg19: chr2-173076840;