chr18-13931828-C-T

Variant names:

• chr18-13931828-C-T
• rs7233911

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 0.368 in 152,078 control chromosomes in the GnomAD database, including 12,276 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 0.37 (12276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 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: 0.368 AC: 55947 AN: 151958 Hom.: 12238 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.368 AC: 56026 AN: 152078 Hom.: 12276 Cov.: 32 AF XY: 0.366 AC XY: 27215 AN XY: 74342

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.336

Alfa AF: 0.321 Hom.: 1509

Bravo AF: 0.382

Asia WGS AF: 0.265 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7233911; hg19: chr18-13931827;