rs8013309

Variant names:

• chr14-35415418-T-C
• rs8013309

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207

ACMG classification

Verdict is Benign. Variant got -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.

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

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.152

Alfa AF: 0.135 Hom.: 1440

Bravo AF: 0.142

Asia WGS AF: 0.223 AC: 775 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	11
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8013309; hg19: chr14-35884624;