chr2-156993114-C-T

Variant names:

• chr2-156993114-C-T
• rs7562882
• ENST00000762467.1:n.195-37634C>T

Variant summary

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

The ENST00000762467.1(ENSG00000287048):​n.195-37634C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,968 control chromosomes in the GnomAD database, including 38,145 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 0.70 (38145 hom., cov: 31)
• Consequence: ENSG00000287048 ENST00000762467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 2 publications found

Genes affected

ENSG00000287048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373710	XR_923509.3	n.71-6184G>A		intron_variant	Intron 1 of 3
LOC105373710	XR_923510.3	n.71-6184G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287048	ENST00000762467.1	n.195-37634C>T		intron_variant	Intron 2 of 2
ENSG00000287048	ENST00000762468.1	n.243-37634C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.700 AC: 106296 AN: 151852 Hom.: 38102 Cov.: 31

Gnomad AFR AF: 0.794

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.700 AC: 106383 AN: 151968 Hom.: 38145 Cov.: 31 AF XY: 0.694 AC XY: 51585 AN XY: 74292

African (AFR) AF: 0.794 AC: 32922 AN: 41472

American (AMR) AF: 0.771 AC: 11777 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2083 AN: 3466

East Asian (EAS) AF: 0.266 AC: 1371 AN: 5152

South Asian (SAS) AF: 0.577 AC: 2772 AN: 4804

European-Finnish (FIN) AF: 0.655 AC: 6906 AN: 10536

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46206 AN: 67954

Other (OTH) AF: 0.698 AC: 1475 AN: 2114

Alfa AF: 0.661 Hom.: 17473

Bravo AF: 0.715

Asia WGS AF: 0.498 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		0.063

Splicing

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

Other links and lift over

dbSNP: rs7562882; hg19: chr2-157849626;