rs558275

Variant names:

• chr12-120759088-A-G
• rs558275
• ENST00000685547.2:n.2536T>C

Variant summary

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

The ENST00000685547.2(ENSG00000255946):​n.2536T>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 0.71 in 152,004 control chromosomes in the GnomAD database, including 39,696 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 0.71 (39696 hom., cov: 30)
• Consequence: ENSG00000255946 ENST00000685547.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 11 publications found

Genes affected

ENSG00000255946 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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
ENSG00000255946	ENST00000685547.2	n.2536T>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000255946	ENST00000542620.2	n.258+2303T>C		intron_variant	Intron 1 of 2	3
ENSG00000255946	ENST00000724268.1	n.304+2303T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107867 AN: 151884 Hom.: 39641 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.710 AC: 107981 AN: 152004 Hom.: 39696 Cov.: 30 AF XY: 0.717 AC XY: 53261 AN XY: 74304

African (AFR) AF: 0.889 AC: 36871 AN: 41480

American (AMR) AF: 0.765 AC: 11679 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2421 AN: 3468

East Asian (EAS) AF: 0.844 AC: 4359 AN: 5162

South Asian (SAS) AF: 0.776 AC: 3738 AN: 4816

European-Finnish (FIN) AF: 0.581 AC: 6130 AN: 10544

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40418 AN: 67948

Other (OTH) AF: 0.685 AC: 1446 AN: 2112

Alfa AF: 0.638 Hom.: 16118

Bravo AF: 0.731

Asia WGS AF: 0.811 AC: 2817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.37
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs558275; hg19: chr12-121196891;