2-112788101-T-C

Variant names:

• chr2-112788101-T-C
• rs3783516
• ENST00000762716.1:n.1503T>C

Variant summary

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

The ENST00000762716.1(ENSG00000299339):​n.1503T>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 0.633 in 152,024 control chromosomes in the GnomAD database, including 30,607 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 0.63 (30607 hom., cov: 32)
• Consequence: ENSG00000299339 ENST00000762716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 20 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762716.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299339	ENST00000762716.1		n.1503T>C		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299339	ENST00000762706.1		n.404+17205T>C		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+17205T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.632 AC: 96059 AN: 151906 Hom.: 30558 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.633 AC: 96164 AN: 152024 Hom.: 30607 Cov.: 32 AF XY: 0.641 AC XY: 47593 AN XY: 74284

African (AFR) AF: 0.634 AC: 26272 AN: 41442

American (AMR) AF: 0.692 AC: 10575 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4061 AN: 5172

South Asian (SAS) AF: 0.604 AC: 2905 AN: 4812

European-Finnish (FIN) AF: 0.718 AC: 7576 AN: 10554

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40574 AN: 67972

Other (OTH) AF: 0.632 AC: 1334 AN: 2110

Alfa AF: 0.627 Hom.: 10447

Bravo AF: 0.634

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.60
PhyloP100		-0.76

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: rs3783516;

hg19: chr2-113545678;