14-68864460-T-C

Variant names:

• chr14-68864460-T-C
• rs445863

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 0.633 in 151,948 control chromosomes in the GnomAD database, including 30,942 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 0.63 (30942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.601

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.718 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96123 AN: 151830 Hom.: 30914 Cov.: 31

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.633 AC: 96191 AN: 151948 Hom.: 30942 Cov.: 31 AF XY: 0.634 AC XY: 47032 AN XY: 74216

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.638

Alfa AF: 0.650 Hom.: 8929

Bravo AF: 0.632

Asia WGS AF: 0.663 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs445863; hg19: chr14-69331177;