rs3858029

Positions:

• chr9-1756470-A-C
• chr9-1756470-A-T

Variant summary

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

The XR_001746599.1(LOC105375951):​n.142+37558A>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 0.382 in 151,992 control chromosomes in the GnomAD database, including 11,320 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 0.38 (11320 hom., cov: 32)
• Consequence: LOC105375951 XR_001746599.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

LOC105375951 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375951	XR_001746599.1	n.142+37558A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57911 AN: 151874 Hom.: 11283 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.382 AC: 58011 AN: 151992 Hom.: 11320 Cov.: 32 AF XY: 0.386 AC XY: 28652 AN XY: 74286

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.382

Alfa AF: 0.380 Hom.: 1896

Bravo AF: 0.391

Asia WGS AF: 0.412 AC: 1433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3858029; hg19: chr9-1756470; COSMIC: COSV69442000;