rs156331

Variant names:

• chr20-1846342-C-A
• rs156331
• ENST00000716594.1:n.951-35118G>T

Variant summary

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

The ENST00000716594.1(ENSG00000286288):​n.951-35118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,184 control chromosomes in the GnomAD database, including 5,411 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 0.25 (5411 hom., cov: 33)
• Consequence: ENSG00000286288 ENST00000716594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.38
• Publications: 7 publications found

Genes affected

ENSG00000286288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716594.1. 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
	ENSG00000286288	ENST00000716594.1		n.951-35118G>T		intron	N/A
	ENSG00000286288	ENST00000844949.1		n.102+28673G>T		intron	N/A
	ENSG00000286288	ENST00000844950.1		n.120+15425G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38748 AN: 152066 Hom.: 5403 Cov.: 33

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.255 AC: 38789 AN: 152184 Hom.: 5411 Cov.: 33 AF XY: 0.255 AC XY: 19006 AN XY: 74400

African (AFR) AF: 0.352 AC: 14621 AN: 41494

American (AMR) AF: 0.206 AC: 3148 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1313 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2123 AN: 5176

South Asian (SAS) AF: 0.221 AC: 1067 AN: 4820

European-Finnish (FIN) AF: 0.238 AC: 2519 AN: 10598

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13145 AN: 68018

Other (OTH) AF: 0.269 AC: 570 AN: 2116

Alfa AF: 0.211 Hom.: 6264

Bravo AF: 0.259

Asia WGS AF: 0.288 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs156331; hg19: chr20-1826988;