rs1110386

chr14-95052503-C-T

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 0.221 in 152,144 control chromosomes in the GnomAD database, including 3,866 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 0.22 (3866 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.284 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: 0.221 AC: 33533 AN: 152026 Hom.: 3858 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.221 AC: 33567 AN: 152144 Hom.: 3866 Cov.: 32 AF XY: 0.217 AC XY: 16118 AN XY: 74386

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.250

Alfa AF: 0.238 Hom.: 5819

Bravo AF: 0.229

Asia WGS AF: 0.314 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.92
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1110386; hg19: chr14-95518840;