rs751355

Positions:

• chr18-9428422-C-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 0.509 in 152,006 control chromosomes in the GnomAD database, including 20,345 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 0.51 (20345 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.633 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: 0.509 AC: 77295 AN: 151886 Hom.: 20318 Cov.: 32

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.509 AC: 77372 AN: 152006 Hom.: 20345 Cov.: 32 AF XY: 0.513 AC XY: 38103 AN XY: 74298

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.522

Alfa AF: 0.534 Hom.: 12029

Bravo AF: 0.507

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751355; hg19: chr18-9428420;