rs109889

Variant names:

• chr2-115851258-C-G
• rs109889
• ENST00000668438.1:n.467-15828G>C

Variant summary

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

The ENST00000668438.1(ENSG00000287451):​n.467-15828G>C variant causes a intron 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: ENSG00000287451 ENST00000668438.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 1 publications found

Genes affected

ENSG00000287451 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668438.1. 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
	ENSG00000287451	ENST00000668438.1		n.467-15828G>C		intron	N/A
	ENSG00000287451	ENST00000773149.1		n.226-13677G>C		intron	N/A

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

African (AFR) AF: 0.148 AC: 6139 AN: 41512

American (AMR) AF: 0.503 AC: 7681 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1691 AN: 3472

East Asian (EAS) AF: 0.172 AC: 891 AN: 5174

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4818

European-Finnish (FIN) AF: 0.550 AC: 5795 AN: 10536

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33205 AN: 67942

Other (OTH) AF: 0.415 AC: 876 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.57
PhyloP100		-0.40

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: rs109889;

hg19: chr2-116608834;