rs1374546

Variant names:

• chr6-55891185-T-C
• rs1374546

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.366 AC: 15145 AN: 41420

American (AMR) AF: 0.188 AC: 2863 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 625 AN: 3466

East Asian (EAS) AF: 0.0992 AC: 513 AN: 5170

South Asian (SAS) AF: 0.128 AC: 616 AN: 4822

European-Finnish (FIN) AF: 0.0995 AC: 1049 AN: 10544

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7292 AN: 67966

Other (OTH) AF: 0.168 AC: 355 AN: 2110

Alfa AF: 0.164 Hom.: 358

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1374546; hg19: chr6-55755983;