rs765529

Variant names:

• chr18-26010890-T-C
• rs765529

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.609 AC: 25194 AN: 41382

American (AMR) AF: 0.231 AC: 3527 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0906 AC: 314 AN: 3464

East Asian (EAS) AF: 0.277 AC: 1434 AN: 5178

South Asian (SAS) AF: 0.112 AC: 543 AN: 4830

European-Finnish (FIN) AF: 0.137 AC: 1448 AN: 10580

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0883 AC: 6005 AN: 67988

Other (OTH) AF: 0.215 AC: 454 AN: 2114

Alfa AF: 0.141 Hom.: 2262

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs765529; hg19: chr18-23590854;