rs7164052

Variant names:

• chr15-48700384-A-C
• rs7164052

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 0.271 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.446 AC: 18495 AN: 41514

American (AMR) AF: 0.206 AC: 3157 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3472

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.121 AC: 585 AN: 4832

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10598

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.232 AC: 15807 AN: 68004

Other (OTH) AF: 0.248 AC: 524 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.93
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7164052; hg19: chr15-48992581;