rs1374546

Positions:

• chr6-55891185-T-C

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 0.188 in 151,966 control chromosomes in the GnomAD database, including 3,758 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 0.19 (3758 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 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: 0.188 AC: 28606 AN: 151848 Hom.: 3756 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0995

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.188 AC: 28640 AN: 151966 Hom.: 3758 Cov.: 31 AF XY: 0.184 AC XY: 13708 AN XY: 74314

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0995

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.168

Alfa AF: 0.157 Hom.: 317

Bravo AF: 0.201

Asia WGS AF: 0.128 AC: 443 AN: 3472

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	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1374546; hg19: chr6-55755983;