rs7398676

Variant names:

• chr12-53236774-G-T
• rs7398676
• ENST00000768428.1:n.99-351G>T

Variant summary

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

The ENST00000768428.1(ENSG00000300047):​n.99-351G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,062 control chromosomes in the GnomAD database, including 13,986 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 0.42 (13986 hom., cov: 32)
• Consequence: ENSG00000300047 ENST00000768428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 13 publications found

Genes affected

ENSG00000300047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.573 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
ENSG00000300047	ENST00000768428.1	n.99-351G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63398 AN: 151944 Hom.: 13970 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.417 AC: 63434 AN: 152062 Hom.: 13986 Cov.: 32 AF XY: 0.416 AC XY: 30950 AN XY: 74318

African (AFR) AF: 0.286 AC: 11876 AN: 41488

American (AMR) AF: 0.418 AC: 6398 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1709 AN: 3468

East Asian (EAS) AF: 0.539 AC: 2786 AN: 5168

South Asian (SAS) AF: 0.591 AC: 2848 AN: 4820

European-Finnish (FIN) AF: 0.421 AC: 4447 AN: 10554

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31970 AN: 67962

Other (OTH) AF: 0.456 AC: 962 AN: 2110

Alfa AF: 0.456 Hom.: 62187

Bravo AF: 0.412

Asia WGS AF: 0.546 AC: 1901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7398676; hg19: chr12-53630558;