2-156949941-A-T

Variant names:

• chr2-156949941-A-T
• rs1033224
• ENST00000762467.1:n.194+63379A>T

Variant summary

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

The ENST00000762467.1(ENSG00000287048):​n.194+63379A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,982 control chromosomes in the GnomAD database, including 6,968 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 0.25 (6968 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000762467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 1 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287048	ENST00000762467.1		n.194+63379A>T		intron	N/A
	ENSG00000287048	ENST00000762468.1		n.242+63379A>T		intron	N/A
	ENSG00000287048	ENST00000762469.1		n.363-20956A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38086 AN: 151864 Hom.: 6947 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.251 AC: 38146 AN: 151982 Hom.: 6968 Cov.: 32 AF XY: 0.252 AC XY: 18709 AN XY: 74298

African (AFR) AF: 0.512 AC: 21183 AN: 41404

American (AMR) AF: 0.253 AC: 3855 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 437 AN: 3470

East Asian (EAS) AF: 0.169 AC: 876 AN: 5174

South Asian (SAS) AF: 0.202 AC: 975 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1742 AN: 10590

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8383 AN: 67978

Other (OTH) AF: 0.246 AC: 520 AN: 2112

Alfa AF: 0.176 Hom.: 455

Bravo AF: 0.270

Asia WGS AF: 0.223 AC: 775 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.69
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1033224; hg19: chr2-157806453;