rs9595100

chr13-44311338-A-G

Variant summary

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

The XR_001749973.2(LOC107984552):n.97A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,118 control chromosomes in the GnomAD database, including 2,633 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 0.16 (2633 hom., cov: 32)
• Consequence: LOC107984552 XR_001749973.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

Genes affected

LOC107984552 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984552	XR_001749973.2	n.97A>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24834 AN: 152000 Hom.: 2633 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.00309

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.163 AC: 24827 AN: 152118 Hom.: 2633 Cov.: 32 AF XY: 0.163 AC XY: 12091 AN XY: 74362

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.00310

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.165

Alfa AF: 0.199 Hom.: 426

Bravo AF: 0.150

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.0
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9595100; hg19: chr13-44885474;