rs2218220

Variant names:

• chr9-21756090-C-T
• rs2218220
• ENST00000765951.1:n.155-34754C>T

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.155-34754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,686 control chromosomes in the GnomAD database, including 28,316 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 0.60 (28316 hom., cov: 30)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 25 publications found

Genes affected

ENSG00000299739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765951.1. 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
	ENSG00000299739	ENST00000765951.1		n.155-34754C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90643 AN: 151568 Hom.: 28260 Cov.: 30

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.598 AC: 90766 AN: 151686 Hom.: 28316 Cov.: 30 AF XY: 0.593 AC XY: 43924 AN XY: 74066

African (AFR) AF: 0.782 AC: 32353 AN: 41374

American (AMR) AF: 0.595 AC: 9055 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1802 AN: 3466

East Asian (EAS) AF: 0.698 AC: 3587 AN: 5142

South Asian (SAS) AF: 0.365 AC: 1744 AN: 4776

European-Finnish (FIN) AF: 0.515 AC: 5420 AN: 10530

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35109 AN: 67886

Other (OTH) AF: 0.570 AC: 1197 AN: 2100

Alfa AF: 0.530 Hom.: 12957

Bravo AF: 0.621

Asia WGS AF: 0.536 AC: 1861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.1
DANN	Benign	0.74
PhyloP100		-0.031

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: rs2218220;

hg19: chr9-21756089;