chr18-25864897-T-C

Variant names:

• chr18-25864897-T-C
• rs1073581

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.538 in 151,796 control chromosomes in the GnomAD database, including 22,330 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 0.54 (22330 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 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: 0.538 AC: 81585 AN: 151680 Hom.: 22317 Cov.: 30

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.538 AC: 81625 AN: 151796 Hom.: 22330 Cov.: 30 AF XY: 0.539 AC XY: 40002 AN XY: 74166

Gnomad4 AFR AF: 0.651

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.528

Alfa AF: 0.457 Hom.: 2906

Bravo AF: 0.537

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.60
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1073581; hg19: chr18-23444861;