chr12-20320824-C-A

Variant names:

• chr12-20320824-C-A
• rs7134375
• ENST00000745914.1:n.185G>T

Variant summary

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

The ENST00000745914.1(ENSG00000297166):​n.185G>T 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 0.393 in 151,726 control chromosomes in the GnomAD database, including 11,952 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 0.39 (11952 hom., cov: 32)
• Consequence: ENSG00000297166 ENST00000745914.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 89 publications found

Genes affected

ENSG00000297166 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369688	XR_931419.3	n.154G>T		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297166	ENST00000745914.1	n.185G>T		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000297166	ENST00000745915.1	n.138G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297166	ENST00000745916.1	n.216G>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297185	ENST00000746036.1	n.16C>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59658 AN: 151608 Hom.: 11951 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.393 AC: 59695 AN: 151726 Hom.: 11952 Cov.: 32 AF XY: 0.390 AC XY: 28875 AN XY: 74104

African (AFR) AF: 0.329 AC: 13638 AN: 41438

American (AMR) AF: 0.421 AC: 6406 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3466

East Asian (EAS) AF: 0.254 AC: 1307 AN: 5136

South Asian (SAS) AF: 0.345 AC: 1652 AN: 4788

European-Finnish (FIN) AF: 0.402 AC: 4228 AN: 10528

Middle Eastern (MID) AF: 0.479 AC: 140 AN: 292

European-Non Finnish (NFE) AF: 0.434 AC: 29443 AN: 67872

Other (OTH) AF: 0.395 AC: 831 AN: 2102

Alfa AF: 0.417 Hom.: 58829

Bravo AF: 0.394

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.86
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs7134375; hg19: chr12-20473758;