rs109889

chr2-115851258-C-G

Variant summary

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

The ENST00000668438.1(ENSG00000287451):n.467-15828G>C 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 0.387 in 152,046 control chromosomes in the GnomAD database, including 13,556 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 0.39 (13556 hom., cov: 32)
• Consequence: ENST00000668438.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.493 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
	ENST00000668438.1	n.467-15828G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58792 AN: 151928 Hom.: 13553 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.387 AC: 58812 AN: 152046 Hom.: 13556 Cov.: 32 AF XY: 0.389 AC XY: 28928 AN XY: 74298

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.415

Alfa AF: 0.432 Hom.: 1929

Bravo AF: 0.370

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs109889; hg19: chr2-116608834;