rs12541654

Positions:

• chr8-22703085-A-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000665743.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000665743.1	n.692T>C		non_coding_transcript_exon_variant	1/2
	ENST00000523627.1	n.164+12772A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.279

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.398

Alfa AF: 0.364 Hom.: 2310

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12541654; hg19: chr8-22560598;