chr14-105537986-T-G

Position:

• chr14-105537986-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.2 in 152,144 control chromosomes in the GnomAD database, including 4,544 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 (4544 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30395 AN: 152026 Hom.: 4513 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.200 AC: 30478 AN: 152144 Hom.: 4544 Cov.: 32 AF XY: 0.201 AC XY: 14960 AN XY: 74386

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.222

Alfa AF: 0.113 Hom.: 722

Bravo AF: 0.215

Asia WGS AF: 0.316 AC: 1098 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12100587; hg19: chr14-106004323;