chr5-18021998-G-A

Position:

• chr5-18021998-G-A

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 0.046 in 152,066 control chromosomes in the GnomAD database, including 197 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 0.046 (197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0694 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: 0.0460 AC: 6996 AN: 151948 Hom.: 196 Cov.: 31

Gnomad AFR AF: 0.0717

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0402

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0320

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0555

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

GnomAD4 genome AF: 0.0460 AC: 6995 AN: 152066 Hom.: 197 Cov.: 31 AF XY: 0.0466 AC XY: 3461 AN XY: 74332

Gnomad4 AFR AF: 0.0715

Gnomad4 AMR AF: 0.0367

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.0320

Gnomad4 NFE AF: 0.0326

Gnomad4 OTH AF: 0.0549

Alfa AF: 0.0378 Hom.: 120

Bravo AF: 0.0476

Asia WGS AF: 0.0530 AC: 183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17839277; hg19: chr5-18022107;