rs7534376

Variant names:

• chr1-55327143-A-G
• rs7534376

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;