rs1667254

Variant names:

• chr18-31606165-C-T
• rs1667254
• ENST00000724044.1:n.285+1208G>A

Variant summary

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

The ENST00000724044.1(ENSG00000294516):​n.285+1208G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,860 control chromosomes in the GnomAD database, including 8,706 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 0.34 (8706 hom., cov: 31)
• Consequence: ENSG00000294516 ENST00000724044.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904277	XR_007066326.1	n.128+1208G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294516	ENST00000724044.1	n.285+1208G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51279 AN: 151742 Hom.: 8696 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.338 AC: 51331 AN: 151860 Hom.: 8706 Cov.: 31 AF XY: 0.335 AC XY: 24877 AN XY: 74192

African (AFR) AF: 0.341 AC: 14106 AN: 41394

American (AMR) AF: 0.341 AC: 5206 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1361 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1668 AN: 5156

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4812

European-Finnish (FIN) AF: 0.257 AC: 2703 AN: 10526

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.342 AC: 23240 AN: 67946

Other (OTH) AF: 0.374 AC: 787 AN: 2104

Alfa AF: 0.350 Hom.: 16360

Bravo AF: 0.343

Asia WGS AF: 0.372 AC: 1299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.40
DANN	Benign	0.39
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1667254; hg19: chr18-29186128;