rs4760673

Positions:

• chr12-47962326-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000624535.1(ENSG00000279840):​n.1144T>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 0.251 in 152,112 control chromosomes in the GnomAD database, including 6,440 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 0.25 (6439 hom., cov: 32)
  • Exomes 𝑓: 0.11 (1 hom.)
• Consequence: ENSG00000279840 ENST00000624535.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569

Genes affected

ENSG00000279840 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 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
ENSG00000279840	ENST00000624535.1	n.1144T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38162 AN: 151952 Hom.: 6430 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.248

GnomAD4 exome AF: 0.114 AC: 5 AN: 44 Hom.: 1 Cov.: 0 AF XY: 0.0938 AC XY: 3 AN XY: 32

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.147

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.251 AC: 38204 AN: 152068 Hom.: 6439 Cov.: 32 AF XY: 0.246 AC XY: 18287 AN XY: 74350

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.245

Alfa AF: 0.171 Hom.: 4989

Bravo AF: 0.267

Asia WGS AF: 0.239 AC: 832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4760673; hg19: chr12-48356109;