rs2218817

Positions:

• chr4-111689850-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000681719.1(ENSG00000248656):​n.352+18397G>A variant causes a intron, non coding transcript 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: ENST00000681719.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000681719.1	n.352+18397G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.307

Alfa AF: 0.316 Hom.: 4357

Bravo AF: 0.327

Asia WGS AF: 0.417 AC: 1450 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2218817; hg19: chr4-112611006;