2-156816316-A-T

Variant names:

• chr2-156816316-A-T
• rs11683474
• ENST00000665531.1:n.45+27541A>T

Variant summary

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

The ENST00000665531.1(ENSG00000287048):​n.45+27541A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,074 control chromosomes in the GnomAD database, including 1,028 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 0.10 (1028 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000665531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665531.1. 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	ENST00000665531.1		n.45+27541A>T		intron	N/A
	ENSG00000287048	ENST00000670545.1		n.109+12869A>T		intron	N/A
	ENSG00000287048	ENST00000762467.1		n.93+12869A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15436 AN: 151956 Hom.: 1027 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0753

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0505

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.101 AC: 15431 AN: 152074 Hom.: 1028 Cov.: 32 AF XY: 0.0977 AC XY: 7262 AN XY: 74340

African (AFR) AF: 0.0385 AC: 1600 AN: 41560

American (AMR) AF: 0.0873 AC: 1334 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0753 AC: 261 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0503 AC: 243 AN: 4830

European-Finnish (FIN) AF: 0.110 AC: 1161 AN: 10546

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10387 AN: 67886

Other (OTH) AF: 0.108 AC: 228 AN: 2108

Alfa AF: 0.0665 Hom.: 102

Bravo AF: 0.0961

Asia WGS AF: 0.0220 AC: 75 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.33
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs11683474; hg19: chr2-157672828;