rs2156010

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985152	XR_007066370.1	n.177+18799C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267699	ENST00000590722.2	n.158-35801G>A		intron_variant	Intron 2 of 8	2		ENSP00000465737.1
ENSG00000267699	ENST00000588256.1	n.334+26556G>A		intron_variant	Intron 3 of 3	4

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.420

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.439

Alfa AF: 0.404 Hom.: 1599

Bravo AF: 0.432

Asia WGS AF: 0.386 AC: 1338 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs2156010; hg19: chr18-48537489;