14-85276014-G-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 0.593 in 151,714 control chromosomes in the GnomAD database, including 28,266 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 0.59 (28266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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 = 0.771 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: 0.593 AC: 89832 AN: 151596 Hom.: 28231 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.593 AC: 89921 AN: 151714 Hom.: 28266 Cov.: 32 AF XY: 0.585 AC XY: 43408 AN XY: 74150

Gnomad4 AFR AF: 0.778

Gnomad4 AMR AF: 0.499

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.0920

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.549

Alfa AF: 0.498 Hom.: 1519

Bravo AF: 0.594

Asia WGS AF: 0.264 AC: 917 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.35
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961166; hg19: chr14-85742358;