rs17602038

Positions:

• chr11-113493969-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_948024.2(LOC105369501):​n.107-2779A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,036 control chromosomes in the GnomAD database, including 6,414 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 0.27 (6414 hom., cov: 32)
• Consequence: LOC105369501 XR_948024.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40

Genes affected

LOC105369501 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369501	XR_948024.2	n.107-2779A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40419 AN: 151918 Hom.: 6417 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.266 AC: 40405 AN: 152036 Hom.: 6414 Cov.: 32 AF XY: 0.256 AC XY: 19025 AN XY: 74324

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.330

Alfa AF: 0.315 Hom.: 1450

Bravo AF: 0.273

Asia WGS AF: 0.131 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17602038; hg19: chr11-113364691;