rs378775

chr6-52976681-C-G

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 0.735 in 152,082 control chromosomes in the GnomAD database, including 41,809 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 0.73 (41809 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.735 AC: 111727 AN: 151964 Hom.: 41810 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.735 AC: 111756 AN: 152082 Hom.: 41809 Cov.: 31 AF XY: 0.736 AC XY: 54752 AN XY: 74344

Gnomad4 AFR AF: 0.604

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.801

Gnomad4 OTH AF: 0.747

Alfa AF: 0.753 Hom.: 5409

Bravo AF: 0.720

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs378775; hg19: chr6-52841479;