chr2-112807389-T-A

Variant names:

• chr2-112807389-T-A
• rs7567619
• ENST00000762706.1:n.404+36493T>A

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+36493T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 150,684 control chromosomes in the GnomAD database, including 7,930 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 0.31 (7930 hom., cov: 29)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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.404+36493T>A		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+36493T>A		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+36493T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.311 AC: 46754 AN: 150576 Hom.: 7914 Cov.: 29

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.311 AC: 46792 AN: 150684 Hom.: 7930 Cov.: 29 AF XY: 0.319 AC XY: 23465 AN XY: 73532

African (AFR) AF: 0.230 AC: 9483 AN: 41208

American (AMR) AF: 0.394 AC: 5954 AN: 15124

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 878 AN: 3460

East Asian (EAS) AF: 0.702 AC: 3579 AN: 5100

South Asian (SAS) AF: 0.333 AC: 1593 AN: 4790

European-Finnish (FIN) AF: 0.396 AC: 3952 AN: 9976

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.301 AC: 20376 AN: 67718

Other (OTH) AF: 0.320 AC: 674 AN: 2104

Alfa AF: 0.137 Hom.: 265

Bravo AF: 0.313

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.32
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs7567619; hg19: chr2-113564966;