rs78546022

chr6-150059748-A-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 0.046 in 152,250 control chromosomes in the GnomAD database, including 190 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 0.046 (190 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0747 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: 0.0461 AC: 7009 AN: 152132 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.0991

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.0432

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0610

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0460 AC: 7009 AN: 152250 Hom.: 190 Cov.: 32 AF XY: 0.0462 AC XY: 3442 AN XY: 74452

Gnomad4 AFR AF: 0.0145

Gnomad4 AMR AF: 0.0500

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.0429

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.0432

Gnomad4 NFE AF: 0.0610

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0528 Hom.: 29

Bravo AF: 0.0443

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78546022; hg19: chr6-150380884;