1-30760633-A-G

Variant names:

• chr1-30760633-A-G
• rs10798801

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 0.64 in 152,044 control chromosomes in the GnomAD database, including 32,092 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 0.64 (32092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 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: 0.639 AC: 97145 AN: 151926 Hom.: 32045 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.640 AC: 97256 AN: 152044 Hom.: 32092 Cov.: 32 AF XY: 0.639 AC XY: 47468 AN XY: 74316

African (AFR) AF: 0.786 AC: 32565 AN: 41454

American (AMR) AF: 0.648 AC: 9900 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2049 AN: 3472

East Asian (EAS) AF: 0.821 AC: 4254 AN: 5182

South Asian (SAS) AF: 0.607 AC: 2931 AN: 4828

European-Finnish (FIN) AF: 0.557 AC: 5883 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37642 AN: 67954

Other (OTH) AF: 0.606 AC: 1282 AN: 2116

Alfa AF: 0.594 Hom.: 10402

Bravo AF: 0.652

Asia WGS AF: 0.701 AC: 2439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10798801; hg19: chr1-31233480; COSMIC: COSV53852867;