rs9576104

chr13-36725155-A-G

Variant summary

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

The XR_001749825.2(LOC102723490):n.595-18446T>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 0.118 in 152,074 control chromosomes in the GnomAD database, including 1,376 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 (1376 hom., cov: 31)
• Consequence: LOC102723490 XR_001749825.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.852

Genes affected

LOC102723490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723490	XR_001749825.2	n.595-18446T>C		intron_variant, non_coding_transcript_variant
LOC102723490	XR_001749824.2	n.595-18446T>C		intron_variant, non_coding_transcript_variant
LOC102723490	XR_001749828.2	n.595-18446T>C		intron_variant, non_coding_transcript_variant
LOC102723490	XR_007063757.1	n.595-18446T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17918 AN: 151956 Hom.: 1374 Cov.: 31

Gnomad AFR AF: 0.0376

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.118 AC: 17926 AN: 152074 Hom.: 1376 Cov.: 31 AF XY: 0.123 AC XY: 9160 AN XY: 74332

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.103

Alfa AF: 0.133 Hom.: 173

Bravo AF: 0.104

Asia WGS AF: 0.242 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	5.3
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9576104; hg19: chr13-37299292;