rs7542755

Variant names:

• chr1-80665095-G-A
• rs7542755

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 0.36 in 151,814 control chromosomes in the GnomAD database, including 12,531 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 0.36 (12531 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.458 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: 0.360 AC: 54641 AN: 151696 Hom.: 12526 Cov.: 32

Gnomad AFR AF: 0.0838

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.360 AC: 54644 AN: 151814 Hom.: 12531 Cov.: 32 AF XY: 0.368 AC XY: 27272 AN XY: 74198

Gnomad4 AFR AF: 0.0836

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.343

Alfa AF: 0.423 Hom.: 8536

Bravo AF: 0.332

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.018
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7542755; hg19: chr1-81130780;