11-102844317-T-C

Variant names:

• chr11-102844317-T-C
• rs522616

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 0.234 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
• Publications: 73 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.200 AC: 8303 AN: 41502

American (AMR) AF: 0.376 AC: 5741 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 796 AN: 3468

East Asian (EAS) AF: 0.373 AC: 1928 AN: 5172

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4818

European-Finnish (FIN) AF: 0.196 AC: 2074 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.207 AC: 14044 AN: 67974

Other (OTH) AF: 0.232 AC: 491 AN: 2114

Alfa AF: 0.221 Hom.: 12369

Bravo AF: 0.247

Asia WGS AF: 0.343 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.9
DANN	Benign	0.67
PhyloP100		-0.052

Splicing

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

Other links and lift over

dbSNP: rs522616; hg19: chr11-102715048;