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: 24 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987026	XR_001746563.3	n.163+11735G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299739	ENST00000765951.1	n.155-34754C>T		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs2218220; hg19: chr9-21756089;