12-133077993-C-T

Variant names:

• chr12-133077993-C-T
• rs595241
• ENST00000624401.1:n.400G>A

Variant summary

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

The ENST00000624401.1(ENSG00000279817):​n.400G>A 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 0.435 in 152,004 control chromosomes in the GnomAD database, including 15,986 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 0.43 (15986 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: ENSG00000279817 ENST00000624401.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 5 publications found

Genes affected

ENSG00000279817 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 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
ENSG00000279817	ENST00000624401.1	n.400G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66025 AN: 151878 Hom.: 15980 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.501

GnomAD4 exome AF: 0.250 AC: 2 AN: 8 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

African (AFR) AC: 0 AN: 0

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: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.435 AC: 66049 AN: 151996 Hom.: 15986 Cov.: 32 AF XY: 0.441 AC XY: 32742 AN XY: 74284

African (AFR) AF: 0.225 AC: 9328 AN: 41466

American (AMR) AF: 0.587 AC: 8971 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3468

East Asian (EAS) AF: 0.777 AC: 4007 AN: 5154

South Asian (SAS) AF: 0.518 AC: 2500 AN: 4822

European-Finnish (FIN) AF: 0.457 AC: 4818 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32822 AN: 67950

Other (OTH) AF: 0.503 AC: 1062 AN: 2112

Alfa AF: 0.471 Hom.: 13044

Bravo AF: 0.439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.1
DANN	Benign	0.82
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs595241; hg19: chr12-133654579;