rs13251447

Variant names:

• chr8-6933188-C-A
• rs13251447
• ENST00000734230.1:n.62+1230C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-6933188-C-A
• chr8-6933188-C-T

Variant summary

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

The ENST00000734230.1(ENSG00000295941):​n.62+1230C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,168 control chromosomes in the GnomAD database, including 3,682 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 0.21 (3682 hom., cov: 33)
• Consequence: ENSG00000295941 ENST00000734230.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842
• Publications: 5 publications found

Genes affected

ENSG00000295941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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
ENSG00000295941	ENST00000734230.1	n.62+1230C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32586 AN: 152050 Hom.: 3688 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.214 AC: 32576 AN: 152168 Hom.: 3682 Cov.: 33 AF XY: 0.211 AC XY: 15726 AN XY: 74386

African (AFR) AF: 0.162 AC: 6746 AN: 41516

American (AMR) AF: 0.177 AC: 2701 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 938 AN: 3472

East Asian (EAS) AF: 0.308 AC: 1597 AN: 5182

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4824

European-Finnish (FIN) AF: 0.189 AC: 2006 AN: 10590

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16568 AN: 67984

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.233 Hom.: 17675

Bravo AF: 0.210

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs13251447; hg19: chr8-6790710;