ENST00000821156.1:n.249-39651T>A

Variant names:

• chr2-75318898-A-T
• rs17011067
• ENST00000821156.1:n.249-39651T>A

Variant summary

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

The ENST00000821156.1(ENSG00000306791):​n.249-39651T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,164 control chromosomes in the GnomAD database, including 1,848 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 0.15 (1848 hom., cov: 32)
• Consequence: ENSG00000306791 ENST00000821156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 4 publications found

Genes affected

ENSG00000306791 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821156.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306791	ENST00000821156.1		n.249-39651T>A		intron	N/A
	ENSG00000306791	ENST00000821157.1		n.173-43761T>A		intron	N/A
	ENSG00000306811	ENST00000821263.1		n.146+26753A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22145 AN: 152046 Hom.: 1845 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.146 AC: 22152 AN: 152164 Hom.: 1848 Cov.: 32 AF XY: 0.145 AC XY: 10820 AN XY: 74400

African (AFR) AF: 0.0635 AC: 2637 AN: 41534

American (AMR) AF: 0.132 AC: 2019 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 990 AN: 3466

East Asian (EAS) AF: 0.157 AC: 813 AN: 5176

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4820

European-Finnish (FIN) AF: 0.133 AC: 1413 AN: 10604

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

European-Non Finnish (NFE) AF: 0.183 AC: 12423 AN: 67978

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.0786 Hom.: 110

Bravo AF: 0.139

Asia WGS AF: 0.213 AC: 738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.43
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs17011067; hg19: chr2-75546024;