chr18-900522-T-G

Variant names:

• chr18-900522-T-G
• rs12961210
• ENST00000582554.2:n.179-5827A>C

Variant summary

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

The ENST00000717225.1(ENSG00000265179):​n.261+4941A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,088 control chromosomes in the GnomAD database, including 6,485 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 0.29 (6485 hom., cov: 32)
• Consequence: ENSG00000265179 ENST00000717225.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 4 publications found

Genes affected

ENSG00000265179 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000717225.1. 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
	ENSG00000265179	ENST00000582554.2	TSL:5	n.179-5827A>C		intron	N/A
	ENSG00000265179	ENST00000717225.1		n.261+4941A>C		intron	N/A
	ENSG00000265179	ENST00000717226.1		n.340+3627A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43879 AN: 151970 Hom.: 6492 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.288 AC: 43865 AN: 152088 Hom.: 6485 Cov.: 32 AF XY: 0.285 AC XY: 21207 AN XY: 74358

African (AFR) AF: 0.267 AC: 11083 AN: 41492

American (AMR) AF: 0.320 AC: 4881 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1163 AN: 3468

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5178

South Asian (SAS) AF: 0.283 AC: 1363 AN: 4812

European-Finnish (FIN) AF: 0.239 AC: 2525 AN: 10566

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20888 AN: 67982

Other (OTH) AF: 0.293 AC: 618 AN: 2112

Alfa AF: 0.307 Hom.: 17718

Bravo AF: 0.294

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.37

Splicing

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: rs12961210;

hg19: chr18-900523;