rs567992

Variant names:

• chr11-106391670-C-T
• rs567992
• XR_947985.1:n.102-17473C>T

Variant summary

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

The XR_947985.1(LOC105369474):​n.102-17473C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,100 control chromosomes in the GnomAD database, including 1,816 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 0.13 (1816 hom., cov: 32)
• Consequence: LOC105369474 XR_947985.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 5 publications found

Genes affected

LOC105369474 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369474	XR_947985.1	n.102-17473C>T		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19760 AN: 151982 Hom.: 1807 Cov.: 32

Gnomad AFR AF: 0.0289

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.130 AC: 19777 AN: 152100 Hom.: 1816 Cov.: 32 AF XY: 0.136 AC XY: 10077 AN XY: 74332

African (AFR) AF: 0.0288 AC: 1197 AN: 41516

American (AMR) AF: 0.289 AC: 4407 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.233 AC: 1199 AN: 5148

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1603 AN: 10574

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9437 AN: 67992

Other (OTH) AF: 0.155 AC: 328 AN: 2112

Alfa AF: 0.140 Hom.: 3677

Bravo AF: 0.137

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.65
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs567992; hg19: chr11-106262397;