12-78442167-A-G

Variant names:

• chr12-78442167-A-G
• rs1449460
• ENST00000716270.1:n.357T>C

Variant summary

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

The ENST00000716270.1(ENSG00000257165):​n.357T>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 0.0619 in 152,114 control chromosomes in the GnomAD database, including 446 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 0.062 (446 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: ENSG00000257165 ENST00000716270.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 3 publications found

Genes affected

ENSG00000257165 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716270.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257165	ENST00000716270.1		n.357T>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000257165	ENST00000716272.1		n.786T>C		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000258084	ENST00000548963.1	TSL:5	n.245+18881A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0620 AC: 9418 AN: 151990 Hom.: 446 Cov.: 32

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0540

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.0689

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

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) AC: 0 AN: 0

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: 0.0619 AC: 9415 AN: 152108 Hom.: 446 Cov.: 32 AF XY: 0.0645 AC XY: 4797 AN XY: 74368

African (AFR) AF: 0.0134 AC: 556 AN: 41534

American (AMR) AF: 0.0666 AC: 1016 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3470

East Asian (EAS) AF: 0.151 AC: 780 AN: 5154

South Asian (SAS) AF: 0.223 AC: 1073 AN: 4814

European-Finnish (FIN) AF: 0.0540 AC: 572 AN: 10600

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4674 AN: 67956

Other (OTH) AF: 0.0682 AC: 144 AN: 2112

Alfa AF: 0.0705 Hom.: 811

Bravo AF: 0.0584

Asia WGS AF: 0.159 AC: 552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.68
PhyloP100		-0.26
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1449460; hg19: chr12-78835947;