18-61777448-T-G

Variant names:

• chr18-61777448-T-G
• rs9959847

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 0.377 in 152,042 control chromosomes in the GnomAD database, including 11,147 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 0.38 (11147 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 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: 0.377 AC: 57230 AN: 151924 Hom.: 11126 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.377 AC: 57295 AN: 152042 Hom.: 11147 Cov.: 31 AF XY: 0.373 AC XY: 27745 AN XY: 74324

African (AFR) AF: 0.469 AC: 19438 AN: 41456

American (AMR) AF: 0.311 AC: 4749 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1053 AN: 5172

South Asian (SAS) AF: 0.276 AC: 1328 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3679 AN: 10568

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24229 AN: 67964

Other (OTH) AF: 0.371 AC: 786 AN: 2116

Alfa AF: 0.348 Hom.: 15438

Bravo AF: 0.378

Asia WGS AF: 0.274 AC: 954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	9.8
DANN	Benign	0.66
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs9959847; hg19: chr18-59444681;