rs242

Variant names:

• chr1-20542967-CT-C
• rs242

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;