1-18098517-A-G

Variant names:

• chr1-18098517-A-G
• rs9804128

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 0.343 in 152,004 control chromosomes in the GnomAD database, including 10,367 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 0.34 (10367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 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: 0.343 AC: 52156 AN: 151884 Hom.: 10356 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.343 AC: 52208 AN: 152004 Hom.: 10367 Cov.: 32 AF XY: 0.344 AC XY: 25552 AN XY: 74310

African (AFR) AF: 0.551 AC: 22859 AN: 41452

American (AMR) AF: 0.255 AC: 3888 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 900 AN: 3470

East Asian (EAS) AF: 0.186 AC: 958 AN: 5156

South Asian (SAS) AF: 0.278 AC: 1337 AN: 4816

European-Finnish (FIN) AF: 0.337 AC: 3566 AN: 10578

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.263 AC: 17843 AN: 67948

Other (OTH) AF: 0.330 AC: 695 AN: 2108

Alfa AF: 0.288 Hom.: 21912

Bravo AF: 0.344

Asia WGS AF: 0.250 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.77
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs9804128; hg19: chr1-18425011; COSMIC: COSV59928762;