rs242

Positions:

• chr1-20542967-CT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The variant allele was found at a frequency of 0.073 in 152,192 control chromosomes in the GnomAD database, including 500 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.073 (500 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0730 AC: 11105 AN: 152076 Hom.: 500 Cov.: 31

Gnomad AFR AF: 0.0192

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0567

Gnomad ASJ AF: 0.0853

Gnomad EAS AF: 0.0564

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.0974

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0730 AC: 11108 AN: 152192 Hom.: 500 Cov.: 31 AF XY: 0.0720 AC XY: 5357 AN XY: 74404

Gnomad4 AFR AF: 0.0192

Gnomad4 AMR AF: 0.0566

Gnomad4 ASJ AF: 0.0853

Gnomad4 EAS AF: 0.0564

Gnomad4 SAS AF: 0.0694

Gnomad4 FIN AF: 0.0974

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0281 Hom.: 28

Bravo AF: 0.0675

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242; hg19: chr1-20869460;