rs1074334

Variant names:

• chr14-86648700-A-G
• rs1074334

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 0.252 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0895 AC: 3715 AN: 41508

American (AMR) AF: 0.334 AC: 5091 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1087 AN: 5166

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4802

European-Finnish (FIN) AF: 0.249 AC: 2627 AN: 10564

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22072 AN: 67952

Other (OTH) AF: 0.301 AC: 635 AN: 2108

Alfa AF: 0.267 Hom.: 795

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
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1074334; hg19: chr14-87115044;