14-54194897-T-C

Variant names:

• chr14-54194897-T-C
• rs8011813

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 0.577 in 151,930 control chromosomes in the GnomAD database, including 26,269 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 0.58 (26269 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.322
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.672 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: 0.577 AC: 87569 AN: 151812 Hom.: 26258 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.577 AC: 87611 AN: 151930 Hom.: 26269 Cov.: 31 AF XY: 0.570 AC XY: 42353 AN XY: 74258

African (AFR) AF: 0.448 AC: 18548 AN: 41402

American (AMR) AF: 0.524 AC: 7987 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2538 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1486 AN: 5172

South Asian (SAS) AF: 0.473 AC: 2269 AN: 4802

European-Finnish (FIN) AF: 0.632 AC: 6677 AN: 10564

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45991 AN: 67960

Other (OTH) AF: 0.593 AC: 1251 AN: 2108

Alfa AF: 0.653 Hom.: 14928

Bravo AF: 0.561

Asia WGS AF: 0.443 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	9.2
DANN	Benign	0.65
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs8011813; hg19: chr14-54661615;