rs439314

chr9-26379842-G-A

Variant summary

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

The XR_001746566.2(LOC105375999):n.342-33554C>T 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 0.185 in 152,076 control chromosomes in the GnomAD database, including 6,732 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 0.19 (6732 hom., cov: 33)
• Consequence: LOC105375999 XR_001746566.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

Genes affected

LOC105375999 (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 (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375999	XR_001746566.2	n.342-33554C>T		intron_variant, non_coding_transcript_variant
LOC105375999	XR_001746565.1	n.372-33554C>T		intron_variant, non_coding_transcript_variant
LOC105375999	XR_001746567.1	n.464-33554C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28067 AN: 151958 Hom.: 6714 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.185 AC: 28135 AN: 152076 Hom.: 6732 Cov.: 33 AF XY: 0.180 AC XY: 13353 AN XY: 74362

Gnomad4 AFR AF: 0.552

Gnomad4 AMR AF: 0.0870

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0881

Gnomad4 FIN AF: 0.0230

Gnomad4 NFE AF: 0.0277

Gnomad4 OTH AF: 0.141

Alfa AF: 0.123 Hom.: 1388

Bravo AF: 0.206

Asia WGS AF: 0.191 AC: 665 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	5.4
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs439314; hg19: chr9-26379840;