chr2-112852309-T-C

Variant names:

• chr2-112852309-T-C
• rs6735739
• ENST00000762706.1:n.405-32949T>C

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.405-32949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,984 control chromosomes in the GnomAD database, including 25,364 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 0.57 (25364 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299339	ENST00000762706.1	n.405-32949T>C		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.500-32949T>C		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.266-32949T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86095 AN: 151866 Hom.: 25367 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.566 AC: 86096 AN: 151984 Hom.: 25364 Cov.: 31 AF XY: 0.560 AC XY: 41568 AN XY: 74286

African (AFR) AF: 0.424 AC: 17579 AN: 41424

American (AMR) AF: 0.498 AC: 7607 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2370 AN: 3472

East Asian (EAS) AF: 0.518 AC: 2679 AN: 5168

South Asian (SAS) AF: 0.408 AC: 1968 AN: 4824

European-Finnish (FIN) AF: 0.596 AC: 6278 AN: 10538

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45519 AN: 67966

Other (OTH) AF: 0.578 AC: 1221 AN: 2112

Alfa AF: 0.516 Hom.: 1674

Bravo AF: 0.556

Asia WGS AF: 0.448 AC: 1558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.7
DANN	Benign	0.34
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs6735739; hg19: chr2-113609886;