rs2658046

Variant names:

• chr18-65454994-A-G
• rs2658046

Your query was ambiguous. Multiple possible variants found:

• chr18-65454994-A-G
• chr18-65454994-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 0.444 in 151,596 control chromosomes in the GnomAD database, including 15,103 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 0.44 (15103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 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: 0.444 AC: 67306 AN: 151484 Hom.: 15085 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.444 AC: 67359 AN: 151596 Hom.: 15103 Cov.: 32 AF XY: 0.444 AC XY: 32895 AN XY: 74084

African (AFR) AF: 0.441 AC: 18262 AN: 41422

American (AMR) AF: 0.400 AC: 6075 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1958 AN: 3466

East Asian (EAS) AF: 0.594 AC: 3057 AN: 5144

South Asian (SAS) AF: 0.465 AC: 2238 AN: 4814

European-Finnish (FIN) AF: 0.402 AC: 4200 AN: 10442

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 29964 AN: 67806

Other (OTH) AF: 0.448 AC: 943 AN: 2104

Alfa AF: 0.429 Hom.: 4145

Bravo AF: 0.450

Asia WGS AF: 0.453 AC: 1567 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.32
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2658046; hg19: chr18-63122230;