rs13295552

Positions:

• chr9-81907834-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007061605.1(LOC105376108):​n.1350-19929T>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 0.0214 in 152,240 control chromosomes in the GnomAD database, including 47 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 0.021 (47 hom., cov: 33)
• Consequence: LOC105376108 XR_007061605.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

Genes affected

LOC105376108 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0214 (3263/152240) while in subpopulation NFE AF= 0.0309 (2101/68022). AF 95% confidence interval is 0.0298. There are 47 homozygotes in gnomad4. There are 1559 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376108	XR_007061605.1	n.1350-19929T>G		intron_variant, non_coding_transcript_variant
LOC105376108	XR_007061602.1	n.1539-19929T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 3263 AN: 152122 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00635

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0223

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.0366

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0214 AC: 3263 AN: 152240 Hom.: 47 Cov.: 33 AF XY: 0.0209 AC XY: 1559 AN XY: 74436

Gnomad4 AFR AF: 0.00633

Gnomad4 AMR AF: 0.0222

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.00207

Gnomad4 FIN AF: 0.0366

Gnomad4 NFE AF: 0.0309

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0239 Hom.: 7

Bravo AF: 0.0201

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13295552; hg19: chr9-84522749;