chr14-53966815-C-T

Variant names:

• chr14-53966815-C-T
• rs10873077

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 0.798 in 152,144 control chromosomes in the GnomAD database, including 49,940 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 0.80 (49940 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121368 AN: 152026 Hom.: 49927 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.798 AC: 121420 AN: 152144 Hom.: 49940 Cov.: 32 AF XY: 0.794 AC XY: 59091 AN XY: 74378

African (AFR) AF: 0.606 AC: 25104 AN: 41440

American (AMR) AF: 0.761 AC: 11639 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3210 AN: 3472

East Asian (EAS) AF: 0.646 AC: 3335 AN: 5166

South Asian (SAS) AF: 0.731 AC: 3527 AN: 4828

European-Finnish (FIN) AF: 0.897 AC: 9512 AN: 10604

Middle Eastern (MID) AF: 0.880 AC: 257 AN: 292

European-Non Finnish (NFE) AF: 0.916 AC: 62329 AN: 68022

Other (OTH) AF: 0.829 AC: 1755 AN: 2116

Alfa AF: 0.878 Hom.: 246056

Bravo AF: 0.782

Asia WGS AF: 0.689 AC: 2398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10873077; hg19: chr14-54433533;