14-77011321-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 0.724 in 152,012 control chromosomes in the GnomAD database, including 43,271 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 0.72 (43271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.865 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: 0.725 AC: 110073 AN: 151892 Hom.: 43274 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.871

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.724 AC: 110094 AN: 152012 Hom.: 43271 Cov.: 31 AF XY: 0.728 AC XY: 54071 AN XY: 74302

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.880

Gnomad4 NFE AF: 0.871

Gnomad4 OTH AF: 0.739

Alfa AF: 0.782 Hom.: 7969

Bravo AF: 0.702

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	6.4
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1120277; hg19: chr14-77477664;