14-78055500-C-T

Variant names:

• chr14-78055500-C-T
• rs11159318

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 0.329 in 152,026 control chromosomes in the GnomAD database, including 8,667 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 0.33 (8667 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49881 AN: 151908 Hom.: 8650 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.329 AC: 49942 AN: 152026 Hom.: 8667 Cov.: 31 AF XY: 0.328 AC XY: 24345 AN XY: 74324

African (AFR) AF: 0.386 AC: 15995 AN: 41466

American (AMR) AF: 0.335 AC: 5111 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3466

East Asian (EAS) AF: 0.589 AC: 3031 AN: 5148

South Asian (SAS) AF: 0.206 AC: 991 AN: 4822

European-Finnish (FIN) AF: 0.305 AC: 3219 AN: 10554

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19724 AN: 67986

Other (OTH) AF: 0.347 AC: 732 AN: 2110

Alfa AF: 0.203 Hom.: 452

Bravo AF: 0.339

Asia WGS AF: 0.386 AC: 1342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.0
DANN	Benign	0.63
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs11159318; hg19: chr14-78521843;