ENST00000825047.1:n.332-36197G>A

Variant names:

• chr2-160859127-G-A
• rs270958
• ENST00000825047.1:n.332-36197G>A

Variant summary

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

The ENST00000825047.1(ENSG00000307318):​n.332-36197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,950 control chromosomes in the GnomAD database, including 10,251 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 0.36 (10251 hom., cov: 31)
• Consequence: ENSG00000307318 ENST00000825047.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.584
• Publications: 4 publications found

Genes affected

ENSG00000307318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825047.1. 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
	ENSG00000307318	ENST00000825047.1		n.332-36197G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54785 AN: 151832 Hom.: 10227 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.361 AC: 54857 AN: 151950 Hom.: 10251 Cov.: 31 AF XY: 0.356 AC XY: 26413 AN XY: 74274

African (AFR) AF: 0.457 AC: 18921 AN: 41418

American (AMR) AF: 0.333 AC: 5089 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1653 AN: 5166

South Asian (SAS) AF: 0.266 AC: 1282 AN: 4814

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10570

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22626 AN: 67922

Other (OTH) AF: 0.365 AC: 772 AN: 2116

Alfa AF: 0.345 Hom.: 15440

Bravo AF: 0.375

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	15
DANN	Benign	0.60
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs270958; hg19: chr2-161715638;