chr11-57210155-C-G

Variant names:

• chr11-57210155-C-G
• rs11228951
• XR_001748217.1:n.1008-15390G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_950120.3(LOC105369309):​n.1194+11886G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,960 control chromosomes in the GnomAD database, including 9,278 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 0.33 (9278 hom., cov: 31)
• Consequence: LOC105369309 XR_950120.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.635
• Publications: 2 publications found

Genes affected

LOC105369309 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49406 AN: 151842 Hom.: 9265 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.391

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.325 AC: 49441 AN: 151960 Hom.: 9278 Cov.: 31 AF XY: 0.336 AC XY: 24937 AN XY: 74256

African (AFR) AF: 0.136 AC: 5626 AN: 41478

American (AMR) AF: 0.395 AC: 6036 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1541 AN: 3470

East Asian (EAS) AF: 0.372 AC: 1914 AN: 5150

South Asian (SAS) AF: 0.482 AC: 2321 AN: 4816

European-Finnish (FIN) AF: 0.525 AC: 5534 AN: 10542

Middle Eastern (MID) AF: 0.410 AC: 119 AN: 290

European-Non Finnish (NFE) AF: 0.371 AC: 25211 AN: 67922

Other (OTH) AF: 0.365 AC: 770 AN: 2110

Alfa AF: 0.207 Hom.: 483

Bravo AF: 0.306

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.48
DANN	Benign	0.74
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs11228951; hg19: chr11-56977629;