rs751355

Variant names:

• chr18-9428422-C-T
• rs751355

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;