12-119965993-C-T

Variant names:

• chr12-119965993-C-T
• rs10774538
• ENST00000828974.1:n.193-9025C>T

Variant summary

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

The ENST00000828974.1(ENSG00000307806):​n.193-9025C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 151,790 control chromosomes in the GnomAD database, including 1,646 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 0.13 (1646 hom., cov: 31)
• Consequence: ENSG00000307806 ENST00000828974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 5 publications found

Genes affected

ENSG00000307806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268087	XR_002957390.2	n.312-9025C>T		intron_variant	Intron 2 of 2
LOC112268087	XR_002957391.2	n.398-9025C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307806	ENST00000828974.1	n.193-9025C>T		intron_variant	Intron 1 of 1
ENSG00000307806	ENST00000828975.1	n.297-9025C>T		intron_variant	Intron 2 of 2
ENSG00000307806	ENST00000828976.1	n.260-9025C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.132 AC: 19987 AN: 151674 Hom.: 1634 Cov.: 31

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.132 AC: 20023 AN: 151790 Hom.: 1646 Cov.: 31 AF XY: 0.136 AC XY: 10107 AN XY: 74152

African (AFR) AF: 0.0801 AC: 3316 AN: 41388

American (AMR) AF: 0.206 AC: 3140 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3468

East Asian (EAS) AF: 0.358 AC: 1845 AN: 5158

South Asian (SAS) AF: 0.166 AC: 798 AN: 4800

European-Finnish (FIN) AF: 0.135 AC: 1418 AN: 10520

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.132 AC: 8947 AN: 67952

Other (OTH) AF: 0.122 AC: 256 AN: 2094

Alfa AF: 0.130 Hom.: 735

Bravo AF: 0.135

Asia WGS AF: 0.261 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.68
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10774538; hg19: chr12-120403797;