rs4760674

Positions:

• chr12-47963231-A-C

Variant summary

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

The ENST00000624535.1(ENSG00000279840):​n.239T>G 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 0.675 in 152,180 control chromosomes in the GnomAD database, including 35,264 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 0.68 (35258 hom., cov: 33)
  • Exomes 𝑓: 0.80 (6 hom.)
• Consequence: ENST00000624535.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.13).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 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
	ENST00000624535.1	n.239T>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102631 AN: 152042 Hom.: 35214 Cov.: 33

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.674

GnomAD4 exome AF: 0.800 AC: 16 AN: 20 Hom.: 6 Cov.: 0 AF XY: 0.700 AC XY: 7 AN XY: 10

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.750

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.675 AC: 102728 AN: 152160 Hom.: 35258 Cov.: 33 AF XY: 0.678 AC XY: 50460 AN XY: 74378

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.675

Alfa AF: 0.626 Hom.: 43431

Bravo AF: 0.685

Asia WGS AF: 0.822 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.5
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4760674; hg19: chr12-48357014;