rs1018040

Variant names:

• chr1-218532472-T-A
• rs1018040

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 0.169 in 151,854 control chromosomes in the GnomAD database, including 2,351 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 0.17 (2351 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25602 AN: 151740 Hom.: 2337 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.169 AC: 25652 AN: 151854 Hom.: 2351 Cov.: 31 AF XY: 0.173 AC XY: 12840 AN XY: 74164

African (AFR) AF: 0.170 AC: 7053 AN: 41422

American (AMR) AF: 0.230 AC: 3512 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 418 AN: 3466

East Asian (EAS) AF: 0.302 AC: 1556 AN: 5154

South Asian (SAS) AF: 0.235 AC: 1126 AN: 4796

European-Finnish (FIN) AF: 0.175 AC: 1832 AN: 10478

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9570 AN: 67974

Other (OTH) AF: 0.168 AC: 354 AN: 2106

Alfa AF: 0.154 Hom.: 233

Bravo AF: 0.176

Asia WGS AF: 0.265 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.88
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1018040; hg19: chr1-218705814;