chr1-55327143-A-G

Variant names:

• chr1-55327143-A-G
• rs7534376

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 0.0902 in 152,210 control chromosomes in the GnomAD database, including 1,502 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 0.090 (1502 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0902 AC: 13713 AN: 152092 Hom.: 1497 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0509

Gnomad ASJ AF: 0.0942

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.00603

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.0865

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

GnomAD4 genome AF: 0.0902 AC: 13733 AN: 152210 Hom.: 1502 Cov.: 32 AF XY: 0.0869 AC XY: 6467 AN XY: 74428

African (AFR) AF: 0.258 AC: 10691 AN: 41470

American (AMR) AF: 0.0508 AC: 778 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0942 AC: 327 AN: 3472

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0234 AC: 113 AN: 4822

European-Finnish (FIN) AF: 0.00603 AC: 64 AN: 10622

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0227 AC: 1542 AN: 68016

Other (OTH) AF: 0.0856 AC: 181 AN: 2114

Alfa AF: 0.0610 Hom.: 331

Bravo AF: 0.101

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.045
DANN	Benign	0.59
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs7534376; hg19: chr1-55792816;