rs2218817

Variant names:

• chr4-111689850-G-A
• rs2218817
• ENST00000681719.1:n.352+18397G>A

Variant summary

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

The ENST00000681719.1(ENSG00000248656):​n.352+18397G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,824 control chromosomes in the GnomAD database, including 8,063 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 0.32 (8063 hom., cov: 31)
• Consequence: ENSG00000248656 ENST00000681719.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 7 publications found

Genes affected

ENSG00000248656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000681719.1. 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
	ENSG00000248656	ENST00000681719.1		n.352+18397G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48854 AN: 151706 Hom.: 8055 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.322 AC: 48874 AN: 151824 Hom.: 8063 Cov.: 31 AF XY: 0.324 AC XY: 24048 AN XY: 74204

African (AFR) AF: 0.342 AC: 14154 AN: 41390

American (AMR) AF: 0.344 AC: 5243 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3468

East Asian (EAS) AF: 0.459 AC: 2360 AN: 5140

South Asian (SAS) AF: 0.470 AC: 2257 AN: 4806

European-Finnish (FIN) AF: 0.241 AC: 2534 AN: 10514

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

European-Non Finnish (NFE) AF: 0.301 AC: 20432 AN: 67938

Other (OTH) AF: 0.307 AC: 648 AN: 2110

Alfa AF: 0.315 Hom.: 4727

Bravo AF: 0.327

Asia WGS AF: 0.417 AC: 1450 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2218817; hg19: chr4-112611006;