rs542338

Variant names:

• chr1-109650144-A-G
• rs542338

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 0.605 in 151,998 control chromosomes in the GnomAD database, including 27,903 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 0.60 (27903 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.605 AC: 91850 AN: 151880 Hom.: 27883 Cov.: 32

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.605 AC: 91923 AN: 151998 Hom.: 27903 Cov.: 32 AF XY: 0.608 AC XY: 45216 AN XY: 74308

African (AFR) AF: 0.596 AC: 24693 AN: 41424

American (AMR) AF: 0.681 AC: 10402 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2204 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3576 AN: 5166

South Asian (SAS) AF: 0.552 AC: 2659 AN: 4816

European-Finnish (FIN) AF: 0.650 AC: 6854 AN: 10548

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39636 AN: 67976

Other (OTH) AF: 0.623 AC: 1315 AN: 2110

Alfa AF: 0.609 Hom.: 8842

Bravo AF: 0.608

Asia WGS AF: 0.633 AC: 2198 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.59
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs542338; hg19: chr1-110192766;