chr14-48058363-T-C

Position:

• chr14-48058363-T-C

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 0.286 in 152,040 control chromosomes in the GnomAD database, including 7,235 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 0.29 (7235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 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: 0.286 AC: 43489 AN: 151922 Hom.: 7235 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.286 AC: 43487 AN: 152040 Hom.: 7235 Cov.: 32 AF XY: 0.288 AC XY: 21421 AN XY: 74312

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.489

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.312

Alfa AF: 0.329 Hom.: 8703

Bravo AF: 0.284

Asia WGS AF: 0.381 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs698322; hg19: chr14-48527566;