rs1113678

Variant names:

• chr18-78794812-A-G
• rs1113678
• ENST00000580487.2:n.1645T>C

Variant summary

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

The ENST00000580487.2(ENSG00000266273):​n.1645T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,146 control chromosomes in the GnomAD database, including 23,632 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 0.53 (23632 hom., cov: 33)
• Consequence: ENSG00000266273 ENST00000580487.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 2 publications found

Genes affected

ENSG00000266273 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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
ENSG00000266273	ENST00000580487.2	n.1645T>C		non_coding_transcript_exon_variant	Exon 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81202 AN: 152028 Hom.: 23604 Cov.: 33

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.534 AC: 81282 AN: 152146 Hom.: 23632 Cov.: 33 AF XY: 0.533 AC XY: 39654 AN XY: 74382

African (AFR) AF: 0.780 AC: 32361 AN: 41504

American (AMR) AF: 0.507 AC: 7753 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3466

East Asian (EAS) AF: 0.299 AC: 1545 AN: 5168

South Asian (SAS) AF: 0.372 AC: 1791 AN: 4820

European-Finnish (FIN) AF: 0.534 AC: 5643 AN: 10570

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29301 AN: 67994

Other (OTH) AF: 0.513 AC: 1086 AN: 2116

Alfa AF: 0.464 Hom.: 29276

Bravo AF: 0.544

Asia WGS AF: 0.349 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.31
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1113678; hg19: chr18-76554812;