rs7534376

chr1-55327143-A-G

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 0.0902 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0508

Gnomad4 ASJ AF: 0.0942

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.00603

Gnomad4 NFE AF: 0.0227

Gnomad4 OTH AF: 0.0856

Alfa AF: 0.0674 Hom.: 257

Bravo AF: 0.101

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.045
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7534376; hg19: chr1-55792816;