rs7542755

Positions:

• chr1-80665095-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;