11-56716389-C-T

Variant names:

• chr11-56716389-C-T
• rs1912373

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 0.2 in 152,064 control chromosomes in the GnomAD database, including 3,288 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 0.20 (3288 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 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: 0.200 AC: 30341 AN: 151946 Hom.: 3280 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.200 AC: 30367 AN: 152064 Hom.: 3288 Cov.: 33 AF XY: 0.192 AC XY: 14300 AN XY: 74334

African (AFR) AF: 0.247 AC: 10237 AN: 41456

American (AMR) AF: 0.160 AC: 2448 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.232 AC: 807 AN: 3472

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5172

South Asian (SAS) AF: 0.0718 AC: 346 AN: 4822

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10578

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14567 AN: 67990

Other (OTH) AF: 0.210 AC: 444 AN: 2112

Alfa AF: 0.216 Hom.: 569

Bravo AF: 0.205

Asia WGS AF: 0.0620 AC: 216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.20
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1912373; hg19: chr11-56483865;