rs12155555

Variant names:

• chr8-26663044-C-T
• rs12155555
• ENST00000811249.1:n.774C>T

Variant summary

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

The ENST00000811249.1(ENSG00000305479):​n.774C>T 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 0.0924 in 152,158 control chromosomes in the GnomAD database, including 763 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 0.092 (763 hom., cov: 32)
• Consequence: ENSG00000305479 ENST00000811249.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281
• Publications: 4 publications found

Genes affected

ENSG00000305479 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 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
ENSG00000305479	ENST00000811249.1	n.774C>T		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14061 AN: 152040 Hom.: 765 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0862

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.00368

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0940

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0924 AC: 14061 AN: 152158 Hom.: 763 Cov.: 32 AF XY: 0.0918 AC XY: 6826 AN XY: 74368

African (AFR) AF: 0.110 AC: 4562 AN: 41522

American (AMR) AF: 0.0861 AC: 1316 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3468

East Asian (EAS) AF: 0.00388 AC: 20 AN: 5150

South Asian (SAS) AF: 0.125 AC: 603 AN: 4824

European-Finnish (FIN) AF: 0.0402 AC: 425 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0940 AC: 6390 AN: 68010

Other (OTH) AF: 0.105 AC: 223 AN: 2116

Alfa AF: 0.0908 Hom.: 136

Bravo AF: 0.0946

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.21
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs12155555; hg19: chr8-26520560;