rs13288912

Positions:

• chr9-35153126-G-C
• chr9-35153126-G-T

Variant summary

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

The XR_007061469.1(LOC124902147):​n.340-1527C>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 0.297 in 151,734 control chromosomes in the GnomAD database, including 8,441 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 0.30 (8441 hom., cov: 29)
• Consequence: LOC124902147 XR_007061469.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

Genes affected

LOC124902147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902147	XR_007061469.1	n.340-1527C>G		intron_variant, non_coding_transcript_variant
LOC124902147	XR_007061468.1	n.340-1523C>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45085 AN: 151616 Hom.: 8435 Cov.: 29

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.297 AC: 45092 AN: 151734 Hom.: 8441 Cov.: 29 AF XY: 0.294 AC XY: 21792 AN XY: 74144

Gnomad4 AFR AF: 0.0968

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.00560

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.321

Alfa AF: 0.224 Hom.: 610

Bravo AF: 0.286

Asia WGS AF: 0.108 AC: 378 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	4.1
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13288912; hg19: chr9-35153123; COSMIC: COSV71459514;