14-54453705-T-G

Variant names:

• chr14-54453705-T-G
• rs11850320

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 0.2 in 151,854 control chromosomes in the GnomAD database, including 3,581 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 0.20 (3581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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: 0.199 AC: 30237 AN: 151738 Hom.: 3572 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0867

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0895

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.200 AC: 30301 AN: 151854 Hom.: 3581 Cov.: 32 AF XY: 0.195 AC XY: 14483 AN XY: 74200

African (AFR) AF: 0.326 AC: 13501 AN: 41386

American (AMR) AF: 0.173 AC: 2638 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0895 AC: 310 AN: 3464

East Asian (EAS) AF: 0.105 AC: 542 AN: 5164

South Asian (SAS) AF: 0.163 AC: 783 AN: 4814

European-Finnish (FIN) AF: 0.138 AC: 1451 AN: 10552

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10609 AN: 67904

Other (OTH) AF: 0.162 AC: 341 AN: 2108

Alfa AF: 0.169 Hom.: 10432

Bravo AF: 0.207

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.1
DANN	Benign	0.66
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs11850320; hg19: chr14-54920423;