rs1104039

chr16-10249181-C-Gchr16-10249181-C-T

Variant summary

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

The XR_001752077.1(LOC105371078):n.330+3133G>C 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 0.279 in 151,742 control chromosomes in the GnomAD database, including 6,331 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 0.28 (6331 hom., cov: 29)
• Consequence: LOC105371078 XR_001752077.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

Genes affected

LOC105371078 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371078	XR_001752077.1	n.330+3133G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42296 AN: 151626 Hom.: 6313 Cov.: 29

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.279 AC: 42339 AN: 151742 Hom.: 6331 Cov.: 29 AF XY: 0.286 AC XY: 21215 AN XY: 74138

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.310

Alfa AF: 0.167 Hom.: 337

Bravo AF: 0.285

Asia WGS AF: 0.436 AC: 1514 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	5.6
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1104039; hg19: chr16-10343038;