chr18-28992466-T-G

Variant names:

• chr18-28992466-T-G
• rs1941207

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 0.317 in 151,944 control chromosomes in the GnomAD database, including 7,786 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 0.32 (7786 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 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: 0.317 AC: 48140 AN: 151826 Hom.: 7794 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.317 AC: 48155 AN: 151944 Hom.: 7786 Cov.: 32 AF XY: 0.323 AC XY: 24007 AN XY: 74282

African (AFR) AF: 0.315 AC: 13067 AN: 41430

American (AMR) AF: 0.301 AC: 4602 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3470

East Asian (EAS) AF: 0.417 AC: 2141 AN: 5132

South Asian (SAS) AF: 0.485 AC: 2338 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3663 AN: 10560

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20565 AN: 67952

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.304 Hom.: 890

Bravo AF: 0.303

Asia WGS AF: 0.436 AC: 1517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.60
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1941207; hg19: chr18-26572430;