rs8013309

Variant names:

• chr14-35415418-T-C
• rs8013309
• ENST00000848537.1:n.241+12031T>C

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+12031T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,230 control chromosomes in the GnomAD database, including 1,582 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 0.14 (1582 hom., cov: 32)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 4 publications found

Genes affected

ENSG00000310246 (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 = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848537.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310246	ENST00000848537.1		n.241+12031T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21347 AN: 152110 Hom.: 1577 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.140 AC: 21360 AN: 152230 Hom.: 1582 Cov.: 32 AF XY: 0.139 AC XY: 10345 AN XY: 74422

African (AFR) AF: 0.148 AC: 6164 AN: 41516

American (AMR) AF: 0.138 AC: 2107 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3472

East Asian (EAS) AF: 0.290 AC: 1503 AN: 5190

South Asian (SAS) AF: 0.135 AC: 649 AN: 4824

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10592

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8563 AN: 68018

Other (OTH) AF: 0.152 AC: 321 AN: 2114

Alfa AF: 0.135 Hom.: 1884

Bravo AF: 0.142

Asia WGS AF: 0.223 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs8013309; hg19: chr14-35884624;