rs7542755

Variant names:

• chr1-80665095-G-A
• rs7542755

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 0.36 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
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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

African (AFR) AF: 0.0836 AC: 3461 AN: 41420

American (AMR) AF: 0.464 AC: 7068 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1401 AN: 5154

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4820

European-Finnish (FIN) AF: 0.662 AC: 6995 AN: 10562

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31391 AN: 67858

Other (OTH) AF: 0.343 AC: 723 AN: 2106

Alfa AF: 0.420 Hom.: 9270

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs7542755; hg19: chr1-81130780;