rs646749

Variant names:

• chr18-60215892-G-A
• rs646749

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 0.453 in 151,886 control chromosomes in the GnomAD database, including 17,316 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 0.45 (17316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370

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 (AFR) allele frequency at 95% confidence interval = 0.671 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: 0.453 AC: 68745 AN: 151768 Hom.: 17281 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.453 AC: 68828 AN: 151886 Hom.: 17316 Cov.: 32 AF XY: 0.447 AC XY: 33153 AN XY: 74208

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.424

Alfa AF: 0.401 Hom.: 6708

Bravo AF: 0.458

Asia WGS AF: 0.333 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs646749; hg19: chr18-57883125;