18-25677222-T-C

Variant names:

• chr18-25677222-T-C
• rs1840440

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 0.534 in 152,086 control chromosomes in the GnomAD database, including 24,275 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 0.53 (24275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.728 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: 0.534 AC: 81162 AN: 151968 Hom.: 24275 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.534 AC: 81178 AN: 152086 Hom.: 24275 Cov.: 32 AF XY: 0.543 AC XY: 40348 AN XY: 74352

African (AFR) AF: 0.256 AC: 10629 AN: 41496

American (AMR) AF: 0.574 AC: 8773 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2161 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2525 AN: 5160

South Asian (SAS) AF: 0.749 AC: 3608 AN: 4818

European-Finnish (FIN) AF: 0.756 AC: 8003 AN: 10586

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43582 AN: 67968

Other (OTH) AF: 0.544 AC: 1146 AN: 2108

Alfa AF: 0.604 Hom.: 130695

Bravo AF: 0.502

Asia WGS AF: 0.598 AC: 2079 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs1840440; hg19: chr18-23257186;