chr11-47919373-T-C

Variant names:

• chr11-47919373-T-C
• rs747782

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 0.255 in 152,012 control chromosomes in the GnomAD database, including 5,695 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 0.26 (5695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82

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 (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.255 AC: 38773 AN: 151894 Hom.: 5696 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.255 AC: 38802 AN: 152012 Hom.: 5695 Cov.: 32 AF XY: 0.255 AC XY: 18981 AN XY: 74320

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.215

Alfa AF: 0.197 Hom.: 6374

Bravo AF: 0.258

Asia WGS AF: 0.188 AC: 655 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	7.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747782; hg19: chr11-47940925;