rs13285401

chr9-35152861-T-C

Variant summary

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

The XR_007061469.1(LOC124902147):n.340-1262A>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 0.549 in 151,598 control chromosomes in the GnomAD database, including 23,845 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 0.55 (23845 hom., cov: 29)
• Consequence: LOC124902147 XR_007061469.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

LOC124902147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902147	XR_007061469.1	n.340-1262A>G		intron_variant, non_coding_transcript_variant
LOC124902147	XR_007061468.1	n.340-1258A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83224 AN: 151478 Hom.: 23826 Cov.: 29

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.549 AC: 83281 AN: 151598 Hom.: 23845 Cov.: 29 AF XY: 0.544 AC XY: 40252 AN XY: 74042

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.557

Alfa AF: 0.587 Hom.: 3359

Bravo AF: 0.543

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13285401; hg19: chr9-35152858;