chr18-2089891-G-A

Variant names:

• chr18-2089891-G-A
• rs491222
• ENST00000579097.1:n.310+36309C>T

Variant summary

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

The ENST00000579097.1(ENSG00000263745):​n.310+36309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,954 control chromosomes in the GnomAD database, including 21,927 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 0.53 (21927 hom., cov: 32)
• Consequence: ENSG00000263745 ENST00000579097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447
• Publications: 3 publications found

Genes affected

ENSG00000263745 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579097.1. 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
	ENSG00000263745	ENST00000579097.1	TSL:2	n.310+36309C>T		intron	N/A
	ENSG00000263745	ENST00000582086.2	TSL:2	n.93+21753C>T		intron	N/A
	ENSG00000263745	ENST00000584867.1	TSL:2	n.196+149902C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79966 AN: 151836 Hom.: 21906 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.527 AC: 80025 AN: 151954 Hom.: 21927 Cov.: 32 AF XY: 0.531 AC XY: 39472 AN XY: 74268

African (AFR) AF: 0.646 AC: 26760 AN: 41428

American (AMR) AF: 0.575 AC: 8786 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1417 AN: 3466

East Asian (EAS) AF: 0.787 AC: 4053 AN: 5148

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4824

European-Finnish (FIN) AF: 0.503 AC: 5315 AN: 10562

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29391 AN: 67934

Other (OTH) AF: 0.532 AC: 1121 AN: 2108

Alfa AF: 0.469 Hom.: 25033

Bravo AF: 0.541

Asia WGS AF: 0.667 AC: 2323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.66
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs491222; hg19: chr18-2089892;