rs751355

Variant names:

• chr18-9428422-C-T
• rs751355

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 0.509 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.373 AC: 15473 AN: 41462

American (AMR) AF: 0.609 AC: 9300 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1761 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3349 AN: 5142

South Asian (SAS) AF: 0.562 AC: 2707 AN: 4820

European-Finnish (FIN) AF: 0.602 AC: 6360 AN: 10570

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36652 AN: 67954

Other (OTH) AF: 0.522 AC: 1102 AN: 2112

Alfa AF: 0.534 Hom.: 13135

Bravo AF: 0.507

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs751355; hg19: chr18-9428420;