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. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.576 AC: 23859 AN: 41446

American (AMR) AF: 0.394 AC: 6031 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 569 AN: 3470

East Asian (EAS) AF: 0.160 AC: 828 AN: 5174

South Asian (SAS) AF: 0.194 AC: 932 AN: 4812

European-Finnish (FIN) AF: 0.272 AC: 2876 AN: 10564

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18169 AN: 67960

Other (OTH) AF: 0.341 AC: 720 AN: 2112

Alfa AF: 0.365 Hom.: 4237

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
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs7154439; hg19: chr14-70265828;