rs7134340

Variant names:

• chr12-93996709-G-A
• rs7134340
• ENST00000786429.1:n.124-305C>T

Variant summary

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

The ENST00000786429.1(ENSG00000257283):​n.124-305C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0726 in 152,140 control chromosomes in the GnomAD database, including 660 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 0.073 (660 hom., cov: 32)
• Consequence: ENSG00000257283 ENST00000786429.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.139
• Publications: 0 publications found

Genes affected

ENSG00000257283 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369912	XR_001749263.2	n.89-305C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257283	ENST00000786429.1	n.124-305C>T		intron_variant	Intron 1 of 3
ENSG00000257283	ENST00000786430.1	n.135-305C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11034 AN: 152022 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0253

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0704

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

GnomAD4 genome AF: 0.0726 AC: 11050 AN: 152140 Hom.: 660 Cov.: 32 AF XY: 0.0730 AC XY: 5433 AN XY: 74376

African (AFR) AF: 0.165 AC: 6855 AN: 41460

American (AMR) AF: 0.0480 AC: 733 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.107 AC: 557 AN: 5186

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4822

European-Finnish (FIN) AF: 0.0437 AC: 463 AN: 10594

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1885 AN: 68012

Other (OTH) AF: 0.0701 AC: 148 AN: 2110

Alfa AF: 0.0510 Hom.: 82

Bravo AF: 0.0758

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.3
DANN	Benign	0.60
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7134340; hg19: chr12-94390485;