rs1376178

chr5-40908799-A-Cchr5-40908799-A-Gchr5-40908799-A-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 0.485 in 151,978 control chromosomes in the GnomAD database, including 19,106 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 0.48 (19106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 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: 0.484 AC: 73570 AN: 151860 Hom.: 19075 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.485 AC: 73661 AN: 151978 Hom.: 19106 Cov.: 32 AF XY: 0.482 AC XY: 35824 AN XY: 74292

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.460

Alfa AF: 0.407 Hom.: 21723

Bravo AF: 0.502

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.6
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1376178; hg19: chr5-40908901;