rs644016

Variant names:

• chr18-57497315-G-A
• rs644016

Your query was ambiguous. Multiple possible variants found:

• chr18-57497315-G-A
• chr18-57497315-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 0.41 in 152,026 control chromosomes in the GnomAD database, including 13,519 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 0.41 (13519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.564 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: 0.410 AC: 62328 AN: 151908 Hom.: 13513 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.410 AC: 62379 AN: 152026 Hom.: 13519 Cov.: 32 AF XY: 0.410 AC XY: 30431 AN XY: 74306

African (AFR) AF: 0.570 AC: 23613 AN: 41424

American (AMR) AF: 0.347 AC: 5297 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2229 AN: 5174

South Asian (SAS) AF: 0.437 AC: 2104 AN: 4818

European-Finnish (FIN) AF: 0.329 AC: 3474 AN: 10572

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22965 AN: 67974

Other (OTH) AF: 0.393 AC: 832 AN: 2116

Alfa AF: 0.356 Hom.: 29405

Bravo AF: 0.418

Asia WGS AF: 0.421 AC: 1462 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs644016; hg19: chr18-55164547; COSMIC: COSV68615125;