rs2658046

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;