11-102844317-T-C

Variant names:

• chr11-102844317-T-C
• rs522616

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 0.234 in 152,116 control chromosomes in the GnomAD database, including 4,583 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 0.23 (4583 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0520

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 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: 0.234 AC: 35592 AN: 151998 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.207

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.234 AC: 35602 AN: 152116 Hom.: 4583 Cov.: 32 AF XY: 0.240 AC XY: 17844 AN XY: 74372

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.207

Gnomad4 OTH AF: 0.232

Alfa AF: 0.218 Hom.: 7051

Bravo AF: 0.247

Asia WGS AF: 0.343 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs522616; hg19: chr11-102715048;