rs1378506

chr5-110055529-G-Achr5-110055529-G-Cchr5-110055529-G-T

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 0.548 in 151,950 control chromosomes in the GnomAD database, including 23,080 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 0.55 (23080 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 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: 0.548 AC: 83185 AN: 151832 Hom.: 23071 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.775

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.548 AC: 83234 AN: 151950 Hom.: 23080 Cov.: 32 AF XY: 0.557 AC XY: 41339 AN XY: 74234

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.539

Alfa AF: 0.552 Hom.: 38829

Bravo AF: 0.540

Asia WGS AF: 0.650 AC: 2256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.25
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1378506; hg19: chr5-109391230;