rs7154439

chr14-69799111-G-Achr14-69799111-G-C

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 0.357 in 152,030 control chromosomes in the GnomAD database, including 11,413 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 0.36 (11413 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.472

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 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: 0.357 AC: 54163 AN: 151912 Hom.: 11375 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.357 AC: 54264 AN: 152030 Hom.: 11413 Cov.: 31 AF XY: 0.353 AC XY: 26264 AN XY: 74304

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.341

Alfa AF: 0.351 Hom.: 2232

Bravo AF: 0.372

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.4
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7154439; hg19: chr14-70265828;