ENST00000731318.1:n.309-17622T>C

Variant names:

• chr18-22565416-T-C
• rs12958098
• ENST00000731318.1:n.309-17622T>C

Variant summary

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

The ENST00000731318.1(ENSG00000295614):​n.309-17622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,084 control chromosomes in the GnomAD database, including 13,625 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 0.38 (13625 hom., cov: 32)
• Consequence: ENSG00000295614 ENST00000731318.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 10 publications found

Genes affected

ENSG00000295614 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000731318.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295614	ENST00000731318.1		n.309-17622T>C		intron	N/A
	ENSG00000295614	ENST00000731322.1		n.398-604T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58269 AN: 151966 Hom.: 13627 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.383 AC: 58266 AN: 152084 Hom.: 13625 Cov.: 32 AF XY: 0.384 AC XY: 28557 AN XY: 74318

African (AFR) AF: 0.120 AC: 4986 AN: 41530

American (AMR) AF: 0.288 AC: 4395 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1774 AN: 3466

East Asian (EAS) AF: 0.483 AC: 2495 AN: 5168

South Asian (SAS) AF: 0.423 AC: 2039 AN: 4816

European-Finnish (FIN) AF: 0.580 AC: 6111 AN: 10536

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34997 AN: 67968

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.345 Hom.: 1231

Bravo AF: 0.351

Asia WGS AF: 0.357 AC: 1240 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12958098; hg19: chr18-20145379;