14-65178532-T-C

Position:

• chr14-65178532-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 0.471 in 151,962 control chromosomes in the GnomAD database, including 18,050 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 0.47 (18050 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.593 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: 0.471 AC: 71576 AN: 151844 Hom.: 18051 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.608

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.471 AC: 71597 AN: 151962 Hom.: 18050 Cov.: 32 AF XY: 0.473 AC XY: 35160 AN XY: 74270

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.608

Gnomad4 EAS AF: 0.365

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.486

Alfa AF: 0.528 Hom.: 32100

Bravo AF: 0.471

Asia WGS AF: 0.431 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.29
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7158173; hg19: chr14-65645250;