11-57210155-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_001748217.1(LOC105369309):​n.1008-15390G>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_001748217.1 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369309	XR_001748217.1	n.1008-15390G>C		intron_variant	Intron 2 of 4
LOC105369309	XR_007062670.1	n.1008-15390G>C		intron_variant	Intron 2 of 6
LOC105369309	XR_007062671.1	n.1008-15390G>C		intron_variant	Intron 2 of 4
LOC105369309	XR_950120.3	n.1194+11886G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;