chr5-1391254-A-G

Variant names:

• chr5-1391254-A-G
• rs12516948

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 0.361 in 152,012 control chromosomes in the GnomAD database, including 10,388 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 (10388 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54842 AN: 151894 Hom.: 10372 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.361 AC: 54901 AN: 152012 Hom.: 10388 Cov.: 33 AF XY: 0.354 AC XY: 26307 AN XY: 74288

African (AFR) AF: 0.436 AC: 18072 AN: 41442

American (AMR) AF: 0.289 AC: 4413 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3468

East Asian (EAS) AF: 0.211 AC: 1087 AN: 5152

South Asian (SAS) AF: 0.223 AC: 1076 AN: 4822

European-Finnish (FIN) AF: 0.289 AC: 3055 AN: 10578

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24453 AN: 67944

Other (OTH) AF: 0.370 AC: 782 AN: 2114

Alfa AF: 0.361 Hom.: 4764

Bravo AF: 0.368

Asia WGS AF: 0.208 AC: 724 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.26
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs12516948; hg19: chr5-1391369;