rs708356

Variant names:

• chr12-129989369-T-C
• rs708356
• ENST00000793815.1:n.299+13792T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-129989369-T-C
• chr12-129989369-T-G

Variant summary

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

The ENST00000793815.1(ENSG00000256298):​n.299+13792T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,832 control chromosomes in the GnomAD database, including 10,839 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 0.36 (10839 hom., cov: 31)
• Consequence: ENSG00000256298 ENST00000793815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 5 publications found

Genes affected

ENSG00000256298 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.507 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
ENSG00000256298	ENST00000793815.1	n.299+13792T>C		intron_variant	Intron 2 of 2
ENSG00000303366	ENST00000793958.1	n.59-15839A>G		intron_variant	Intron 1 of 1
ENSG00000303366	ENST00000793959.1	n.106+13397A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55224 AN: 151714 Hom.: 10807 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.364 AC: 55306 AN: 151832 Hom.: 10839 Cov.: 31 AF XY: 0.358 AC XY: 26569 AN XY: 74194

African (AFR) AF: 0.513 AC: 21230 AN: 41382

American (AMR) AF: 0.254 AC: 3872 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1273 AN: 5150

South Asian (SAS) AF: 0.370 AC: 1774 AN: 4800

European-Finnish (FIN) AF: 0.291 AC: 3071 AN: 10558

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.322 AC: 21898 AN: 67918

Other (OTH) AF: 0.319 AC: 671 AN: 2102

Alfa AF: 0.331 Hom.: 33561

Bravo AF: 0.363

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs708356; hg19: chr12-130473914;