rs1378506

Variant names:

• chr5-110055529-G-A
• rs1378506

Your query was ambiguous. Multiple possible variants found:

• chr5-110055529-G-A
• chr5-110055529-G-C
• chr5-110055529-G-T

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 0.548 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.480 AC: 19906 AN: 41468

American (AMR) AF: 0.585 AC: 8915 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1924 AN: 3460

East Asian (EAS) AF: 0.776 AC: 3998 AN: 5154

South Asian (SAS) AF: 0.645 AC: 3107 AN: 4818

European-Finnish (FIN) AF: 0.603 AC: 6362 AN: 10548

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37362 AN: 67948

Other (OTH) AF: 0.539 AC: 1137 AN: 2110

Alfa AF: 0.551 Hom.: 89169

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1378506; hg19: chr5-109391230;