rs13294895

Positions:

• chr9-108074895-C-T

Variant summary

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

The XR_007061722.1(LOC105376214):​n.721-21601G>A 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 0.122 in 152,184 control chromosomes in the GnomAD database, including 1,392 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 0.12 (1392 hom., cov: 33)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.721-21601G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.721-21601G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.721-21601G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18612 AN: 152066 Hom.: 1395 Cov.: 33

Gnomad AFR AF: 0.0338

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0162

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.122 AC: 18609 AN: 152184 Hom.: 1392 Cov.: 33 AF XY: 0.121 AC XY: 9002 AN XY: 74404

Gnomad4 AFR AF: 0.0337

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0162

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.128

Alfa AF: 0.151 Hom.: 598

Bravo AF: 0.115

Asia WGS AF: 0.0580 AC: 203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13294895; hg19: chr9-110837176;