rs12541654

Variant names:

• chr8-22703085-A-G
• rs12541654
• ENST00000665743.1:n.692T>C

Variant summary

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

The ENST00000665743.1(ENSG00000287812):​n.692T>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 0.388 in 151,852 control chromosomes in the GnomAD database, including 11,998 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 0.39 (11998 hom., cov: 31)
• Consequence: ENSG00000287812 ENST00000665743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65
• Publications: 4 publications found

Genes affected

ENSG00000287812 (HGNC:):

ENSG00000253125 (HGNC:58186):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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
ENSG00000287812	ENST00000665743.1	n.692T>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000253125	ENST00000523627.1	n.164+12772A>G		intron_variant	Intron 1 of 4	4
ENSG00000287812	ENST00000810467.1	n.168-116T>C		intron_variant	Intron 1 of 2
ENSG00000287812	ENST00000810468.1	n.52-116T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58810 AN: 151734 Hom.: 11980 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.388 AC: 58874 AN: 151852 Hom.: 11998 Cov.: 31 AF XY: 0.383 AC XY: 28429 AN XY: 74202

African (AFR) AF: 0.494 AC: 20422 AN: 41360

American (AMR) AF: 0.477 AC: 7283 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1427 AN: 3472

East Asian (EAS) AF: 0.279 AC: 1442 AN: 5170

South Asian (SAS) AF: 0.299 AC: 1434 AN: 4804

European-Finnish (FIN) AF: 0.285 AC: 3009 AN: 10540

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22647 AN: 67920

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.402 Hom.: 5983

Bravo AF: 0.408

Asia WGS AF: 0.328 AC: 1142 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	19
DANN	Benign	0.71
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs12541654; hg19: chr8-22560598;