rs1374546

Variant names:

• chr6-55891185-T-C
• rs1374546

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;