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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.448

Alfa AF: 0.434 Hom.: 2551

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2658046; hg19: chr18-63122230;