rs1074334

Positions:

• chr14-86648700-A-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 0.252 in 152,028 control chromosomes in the GnomAD database, including 5,701 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 0.25 (5701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.326 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: 0.252 AC: 38308 AN: 151908 Hom.: 5701 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.252 AC: 38317 AN: 152028 Hom.: 5701 Cov.: 32 AF XY: 0.252 AC XY: 18716 AN XY: 74296

Gnomad4 AFR AF: 0.0895

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.301

Alfa AF: 0.274 Hom.: 789

Bravo AF: 0.251

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1074334; hg19: chr14-87115044;