rs7164052

Positions:

• chr15-48700384-A-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 0.271 in 152,226 control chromosomes in the GnomAD database, including 6,621 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 0.27 (6621 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.447

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41165 AN: 152108 Hom.: 6604 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.271 AC: 41220 AN: 152226 Hom.: 6621 Cov.: 32 AF XY: 0.261 AC XY: 19438 AN XY: 74426

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.248

Alfa AF: 0.258 Hom.: 732

Bravo AF: 0.283

Asia WGS AF: 0.0980 AC: 344 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7164052; hg19: chr15-48992581;