rs1000585

Variant names:

• chr2-75596036-G-A
• rs1000585

Your query was ambiguous. Multiple possible variants found:

• chr2-75596036-G-A
• chr2-75596036-G-C

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 0.558 in 148,694 control chromosomes in the GnomAD database, including 23,287 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 0.56 (23287 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 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: 0.558 AC: 82988 AN: 148596 Hom.: 23278 Cov.: 25

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.558 AC: 83039 AN: 148694 Hom.: 23287 Cov.: 25 AF XY: 0.558 AC XY: 40367 AN XY: 72302

African (AFR) AF: 0.495 AC: 19910 AN: 40256

American (AMR) AF: 0.574 AC: 8612 AN: 15008

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1484 AN: 3452

East Asian (EAS) AF: 0.592 AC: 2996 AN: 5058

South Asian (SAS) AF: 0.578 AC: 2710 AN: 4690

European-Finnish (FIN) AF: 0.580 AC: 5557 AN: 9588

Middle Eastern (MID) AF: 0.560 AC: 159 AN: 284

European-Non Finnish (NFE) AF: 0.592 AC: 39922 AN: 67398

Other (OTH) AF: 0.564 AC: 1161 AN: 2058

Alfa AF: 0.574 Hom.: 40754

Bravo AF: 0.549

Asia WGS AF: 0.625 AC: 2173 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs1000585; hg19: chr2-75823162;