rs765529

Positions:

• chr18-26010890-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.257 in 152,018 control chromosomes in the GnomAD database, including 8,904 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 0.26 (8904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38961 AN: 151900 Hom.: 8875 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0906

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0883

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.257 AC: 39044 AN: 152018 Hom.: 8904 Cov.: 32 AF XY: 0.255 AC XY: 18976 AN XY: 74326

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.0906

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0883

Gnomad4 OTH AF: 0.215

Alfa AF: 0.125 Hom.: 1259

Bravo AF: 0.282

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	21
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs765529; hg19: chr18-23590854;