2-18628463-G-T

Variant names:

• chr2-18628463-G-T
• rs1445128
• ENST00000805686.1:n.480-15707G>T

Variant summary

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

The ENST00000805686.1(ENSG00000304698):​n.480-15707G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,096 control chromosomes in the GnomAD database, including 18,219 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 0.47 (18219 hom., cov: 33)
• Consequence: ENSG00000304698 ENST00000805686.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 3 publications found

Genes affected

ENSG00000304698 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373456	XR_001739304.3	n.723-15707G>T		intron_variant	Intron 2 of 5
LOC105373456	XR_001739311.2	n.238-15707G>T		intron_variant	Intron 1 of 4
LOC105373456	XR_007086227.1	n.238-15707G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304698	ENST00000805686.1	n.480-15707G>T		intron_variant	Intron 2 of 3
ENSG00000304698	ENST00000805687.1	n.465-15707G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71930 AN: 151978 Hom.: 18187 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.474 AC: 72020 AN: 152096 Hom.: 18219 Cov.: 33 AF XY: 0.473 AC XY: 35167 AN XY: 74344

African (AFR) AF: 0.631 AC: 26175 AN: 41500

American (AMR) AF: 0.556 AC: 8499 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1378 AN: 3470

East Asian (EAS) AF: 0.639 AC: 3296 AN: 5162

South Asian (SAS) AF: 0.265 AC: 1278 AN: 4820

European-Finnish (FIN) AF: 0.341 AC: 3605 AN: 10582

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26302 AN: 67972

Other (OTH) AF: 0.463 AC: 977 AN: 2112

Alfa AF: 0.401 Hom.: 6569

Bravo AF: 0.501

Asia WGS AF: 0.469 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.68
DANN	Benign	0.24
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1445128; hg19: chr2-18809729;