rs1607412

Variant names:

• chr18-28912764-C-T
• rs1607412
• ENST00000815223.1:n.326-6385C>T

Variant summary

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

The ENST00000815223.1(ENSG00000306092):​n.326-6385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,956 control chromosomes in the GnomAD database, including 15,516 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 0.43 (15516 hom., cov: 32)
• Consequence: ENSG00000306092 ENST00000815223.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 1 publications found

Genes affected

ENSG00000306092 (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 (NFE) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306092	ENST00000815223.1	n.326-6385C>T		intron_variant	Intron 1 of 2
ENSG00000306092	ENST00000815224.1	n.186-6385C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66003 AN: 151840 Hom.: 15517 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.435 AC: 66025 AN: 151956 Hom.: 15516 Cov.: 32 AF XY: 0.429 AC XY: 31887 AN XY: 74272

African (AFR) AF: 0.272 AC: 11255 AN: 41434

American (AMR) AF: 0.447 AC: 6818 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1156 AN: 5162

South Asian (SAS) AF: 0.368 AC: 1776 AN: 4830

European-Finnish (FIN) AF: 0.451 AC: 4763 AN: 10560

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36484 AN: 67944

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.492 Hom.: 28754

Bravo AF: 0.431

Asia WGS AF: 0.314 AC: 1095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.1
DANN	Benign	0.65
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1607412; hg19: chr18-26492729;