rs574545

Positions:

• chr6-94128228-C-G
• chr6-94128228-C-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 0.428 in 151,134 control chromosomes in the GnomAD database, including 14,258 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 0.43 (14258 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64568 AN: 151014 Hom.: 14252 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.428 AC: 64616 AN: 151134 Hom.: 14258 Cov.: 31 AF XY: 0.426 AC XY: 31408 AN XY: 73788

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.435

Alfa AF: 0.299 Hom.: 748

Bravo AF: 0.420

Asia WGS AF: 0.256 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	6.6
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574545; hg19: chr6-94837946;