14-68864460-T-C

Variant names:

• chr14-68864460-T-C
• rs445863

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.540 AC: 22376 AN: 41416

American (AMR) AF: 0.730 AC: 11132 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2182 AN: 3472

East Asian (EAS) AF: 0.519 AC: 2668 AN: 5144

South Asian (SAS) AF: 0.697 AC: 3355 AN: 4812

European-Finnish (FIN) AF: 0.647 AC: 6829 AN: 10562

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45520 AN: 67972

Other (OTH) AF: 0.638 AC: 1343 AN: 2106

Alfa AF: 0.656 Hom.: 15567

Bravo AF: 0.632

Asia WGS AF: 0.663 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs445863; hg19: chr14-69331177;