2-156949639-T-C

Variant names:

• chr2-156949639-T-C
• rs1033225
• ENST00000762467.1:n.194+63077T>C

Variant summary

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

The ENST00000762467.1(ENSG00000287048):​n.194+63077T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 151,940 control chromosomes in the GnomAD database, including 9,044 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 0.28 (9044 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000762467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.594 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762467.1. 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
	ENSG00000287048	ENST00000762467.1		n.194+63077T>C		intron	N/A
	ENSG00000287048	ENST00000762468.1		n.242+63077T>C		intron	N/A
	ENSG00000287048	ENST00000762469.1		n.363-21258T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41931 AN: 151822 Hom.: 9019 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.276 AC: 41997 AN: 151940 Hom.: 9044 Cov.: 32 AF XY: 0.276 AC XY: 20491 AN XY: 74272

African (AFR) AF: 0.600 AC: 24849 AN: 41386

American (AMR) AF: 0.261 AC: 3986 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 436 AN: 3466

East Asian (EAS) AF: 0.169 AC: 870 AN: 5154

South Asian (SAS) AF: 0.202 AC: 973 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1738 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8400 AN: 67974

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.253 Hom.: 1667

Bravo AF: 0.299

Asia WGS AF: 0.226 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.5
DANN	Benign	0.74
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1033225; hg19: chr2-157806151;