rs4760674

Variant names:

• chr12-47963231-A-C
• rs4760674
• ENST00000624535.1:n.239T>G

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000279840 ENST00000624535.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 21 publications found

Genes affected

ENSG00000279840 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000279840	ENST00000624535.1	n.239T>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 9 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.755 AC: 31350 AN: 41510

American (AMR) AF: 0.704 AC: 10763 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1898 AN: 3468

East Asian (EAS) AF: 0.979 AC: 5073 AN: 5182

South Asian (SAS) AF: 0.737 AC: 3556 AN: 4828

European-Finnish (FIN) AF: 0.613 AC: 6484 AN: 10574

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41484 AN: 67982

Other (OTH) AF: 0.675 AC: 1427 AN: 2114

Alfa AF: 0.634 Hom.: 103011

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
PhyloP100		-0.64
PromoterAI		0.0086	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4760674; hg19: chr12-48357014;