11-93003300-G-C

Variant names:

• chr11-93003300-G-C
• rs271041

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 0.029 in 151,902 control chromosomes in the GnomAD database, including 105 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 0.029 (105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.0561 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: 0.0290 AC: 4396 AN: 151792 Hom.: 105 Cov.: 32

Gnomad AFR AF: 0.0579

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0119

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0292

Gnomad SAS AF: 0.0297

Gnomad FIN AF: 0.0524

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.0131

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0290 AC: 4407 AN: 151902 Hom.: 105 Cov.: 32 AF XY: 0.0303 AC XY: 2252 AN XY: 74216

African (AFR) AF: 0.0580 AC: 2405 AN: 41476

American (AMR) AF: 0.0119 AC: 181 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3466

East Asian (EAS) AF: 0.0292 AC: 151 AN: 5168

South Asian (SAS) AF: 0.0299 AC: 144 AN: 4814

European-Finnish (FIN) AF: 0.0524 AC: 549 AN: 10482

Middle Eastern (MID) AF: 0.0208 AC: 6 AN: 288

European-Non Finnish (NFE) AF: 0.0131 AC: 887 AN: 67940

Other (OTH) AF: 0.0227 AC: 48 AN: 2110

Alfa AF: 0.00922 Hom.: 0

Bravo AF: 0.0265

Asia WGS AF: 0.0370 AC: 127 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.75
DANN	Benign	0.47
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs271041; hg19: chr11-92736466;