rs11083271

Variant names:

• chr18-28346095-C-T
• rs11083271

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 0.279 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
• Publications: 10 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 (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

African (AFR) AF: 0.124 AC: 5143 AN: 41510

American (AMR) AF: 0.320 AC: 4879 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3466

East Asian (EAS) AF: 0.416 AC: 2144 AN: 5150

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4814

European-Finnish (FIN) AF: 0.303 AC: 3200 AN: 10560

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22771 AN: 67940

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.318 Hom.: 21359

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
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs11083271; hg19: chr18-25926059;