rs7154439

Variant names:

• chr14-69799111-G-A
• rs7154439

Your query was ambiguous. Multiple possible variants found:

• chr14-69799111-G-A
• chr14-69799111-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;