rs8015351

chr14-49421667-A-Gchr14-49421667-A-T

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 0.409 in 152,106 control chromosomes in the GnomAD database, including 16,327 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 0.41 (16327 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62145 AN: 151988 Hom.: 16283 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.409 AC: 62255 AN: 152106 Hom.: 16327 Cov.: 32 AF XY: 0.406 AC XY: 30226 AN XY: 74362

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.389

Alfa AF: 0.228 Hom.: 791

Bravo AF: 0.441

Asia WGS AF: 0.376 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8015351; hg19: chr14-49888385;