rs1667255

Variant names:

• chr18-31607316-A-C
• rs1667255
• ENST00000724044.1:n.285+57T>G

Your query was ambiguous. Multiple possible variants found:

• chr18-31607316-A-C
• chr18-31607316-A-G
• chr18-31607316-A-T

Variant summary

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

The ENST00000724044.1(ENSG00000294516):​n.285+57T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 151,374 control chromosomes in the GnomAD database, including 18,780 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 0.48 (18780 hom., cov: 30)
• Consequence: ENSG00000294516 ENST00000724044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 39 publications found

Genes affected

ENSG00000294516 (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 (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904277	XR_007066326.1	n.128+57T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294516	ENST00000724044.1	n.285+57T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71912 AN: 151258 Hom.: 18731 Cov.: 30

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.476 AC: 72030 AN: 151374 Hom.: 18780 Cov.: 30 AF XY: 0.471 AC XY: 34832 AN XY: 73888

African (AFR) AF: 0.703 AC: 29034 AN: 41282

American (AMR) AF: 0.475 AC: 7227 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1522 AN: 3470

East Asian (EAS) AF: 0.404 AC: 2072 AN: 5134

South Asian (SAS) AF: 0.414 AC: 1986 AN: 4794

European-Finnish (FIN) AF: 0.273 AC: 2834 AN: 10364

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25809 AN: 67788

Other (OTH) AF: 0.483 AC: 1022 AN: 2116

Alfa AF: 0.411 Hom.: 55846

Bravo AF: 0.502

Asia WGS AF: 0.450 AC: 1570 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	8.1
DANN	Benign	0.75
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs1667255; hg19: chr18-29187279;