1-98769310-G-A

Variant names:

• chr1-98769310-G-A
• rs1545835

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 0.715 in 151,926 control chromosomes in the GnomAD database, including 40,165 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 0.71 (40165 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.805 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: 0.715 AC: 108506 AN: 151808 Hom.: 40160 Cov.: 31

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.717

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

GnomAD4 genome AF: 0.715 AC: 108564 AN: 151926 Hom.: 40165 Cov.: 31 AF XY: 0.717 AC XY: 53240 AN XY: 74248

African (AFR) AF: 0.557 AC: 23049 AN: 41376

American (AMR) AF: 0.691 AC: 10527 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2650 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1758 AN: 5136

South Asian (SAS) AF: 0.820 AC: 3948 AN: 4812

European-Finnish (FIN) AF: 0.854 AC: 9057 AN: 10602

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55102 AN: 67964

Other (OTH) AF: 0.717 AC: 1516 AN: 2114

Alfa AF: 0.751 Hom.: 5642

Bravo AF: 0.690

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1545835; hg19: chr1-99234866;