rs2156010

Variant names:

• chr18-51011119-G-A
• rs2156010
• ENST00000590722.2:n.158-35801G>A

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.158-35801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,884 control chromosomes in the GnomAD database, including 13,752 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 0.42 (13752 hom., cov: 32)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247
• Publications: 1 publications found

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590722.2. 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
	ENSG00000267699	ENST00000590722.2	TSL:2	n.158-35801G>A		intron	N/A	ENSP00000465737.1	E7EUB6
	ENSG00000267699	ENST00000588256.1	TSL:4	n.334+26556G>A		intron	N/A
	ENSG00000289868	ENST00000797254.1		n.162+18799C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64058 AN: 151766 Hom.: 13734 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.422 AC: 64137 AN: 151884 Hom.: 13752 Cov.: 32 AF XY: 0.420 AC XY: 31138 AN XY: 74218

African (AFR) AF: 0.487 AC: 20161 AN: 41416

American (AMR) AF: 0.403 AC: 6147 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1455 AN: 3466

East Asian (EAS) AF: 0.454 AC: 2343 AN: 5166

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4822

European-Finnish (FIN) AF: 0.410 AC: 4310 AN: 10508

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26837 AN: 67930

Other (OTH) AF: 0.439 AC: 924 AN: 2104

Alfa AF: 0.408 Hom.: 1692

Bravo AF: 0.432

Asia WGS AF: 0.386 AC: 1338 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.50
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2156010;

hg19: chr18-48537489;