rs1998008

Variant names:

• chr1-115037919-A-C
• rs1998008

Your query was ambiguous. Multiple possible variants found:

• chr1-115037919-A-C
• chr1-115037919-A-T

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 0.458 in 152,048 control chromosomes in the GnomAD database, including 16,207 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 0.46 (16207 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69645 AN: 151930 Hom.: 16206 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.458 AC: 69686 AN: 152048 Hom.: 16207 Cov.: 32 AF XY: 0.453 AC XY: 33634 AN XY: 74300

African (AFR) AF: 0.422 AC: 17515 AN: 41478

American (AMR) AF: 0.417 AC: 6374 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.540 AC: 1874 AN: 3468

East Asian (EAS) AF: 0.500 AC: 2577 AN: 5154

South Asian (SAS) AF: 0.388 AC: 1873 AN: 4832

European-Finnish (FIN) AF: 0.398 AC: 4200 AN: 10556

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33700 AN: 67964

Other (OTH) AF: 0.476 AC: 1006 AN: 2112

Alfa AF: 0.484 Hom.: 30719

Bravo AF: 0.461

Asia WGS AF: 0.417 AC: 1452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1998008; hg19: chr1-115580540; COSMIC: COSV56655091;