rs1014922

chr15-94622351-T-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 0.153 in 152,152 control chromosomes in the GnomAD database, including 2,417 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 0.15 (2417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 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: 0.153 AC: 23231 AN: 152036 Hom.: 2408 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0846

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.153 AC: 23278 AN: 152152 Hom.: 2417 Cov.: 32 AF XY: 0.151 AC XY: 11236 AN XY: 74422

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.0817

Gnomad4 NFE AF: 0.0846

Gnomad4 OTH AF: 0.163

Alfa AF: 0.133 Hom.: 487

Bravo AF: 0.165

Asia WGS AF: 0.224 AC: 777 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	4.5
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1014922; hg19: chr15-95165580;