rs16931831

Variant names:

• chr11-15708008-C-T
• rs16931831
• XR_002957240.2:n.322G>A

Variant summary

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

The XR_002957240.2(LOC105376567):​n.322G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,184 control chromosomes in the GnomAD database, including 4,806 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 0.24 (4806 hom., cov: 32)
• Consequence: LOC105376567 XR_002957240.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 7 publications found

Genes affected

LOC105376567 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376567	XR_002957240.2	n.322G>A		non_coding_transcript_exon_variant	Exon 1 of 5
LOC105376567	XR_001748140.2	n.573-3388G>A		intron_variant	Intron 4 of 6
LOC105376567	XR_001748141.2	n.260-3388G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254645	ENST00000524613.1	n.448-914G>A		intron_variant	Intron 4 of 8	5
ENSG00000254645	ENST00000663676.1	n.498-914G>A		intron_variant	Intron 4 of 7
ENSG00000254645	ENST00000727850.1	n.287-3388G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35840 AN: 152066 Hom.: 4800 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0847

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.236 AC: 35870 AN: 152184 Hom.: 4806 Cov.: 32 AF XY: 0.239 AC XY: 17767 AN XY: 74400

African (AFR) AF: 0.345 AC: 14336 AN: 41506

American (AMR) AF: 0.214 AC: 3271 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.213 AC: 1104 AN: 5180

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4824

European-Finnish (FIN) AF: 0.339 AC: 3591 AN: 10588

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11588 AN: 67996

Other (OTH) AF: 0.235 AC: 496 AN: 2110

Alfa AF: 0.189 Hom.: 3994

Bravo AF: 0.238

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.2
DANN	Benign	0.70
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs16931831; hg19: chr11-15729554;