rs11083271

Variant names:

• chr18-28346095-C-T
• rs11083271

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 0.279 in 152,020 control chromosomes in the GnomAD database, including 6,607 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 0.28 (6607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 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: 0.279 AC: 42413 AN: 151902 Hom.: 6605 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.279 AC: 42422 AN: 152020 Hom.: 6607 Cov.: 33 AF XY: 0.281 AC XY: 20898 AN XY: 74266

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.333

Alfa AF: 0.331 Hom.: 14966

Bravo AF: 0.274

Asia WGS AF: 0.374 AC: 1298 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	4.4
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11083271; hg19: chr18-25926059;