rs3118515

Positions:

• chr9-134544468-G-A
• chr9-134544468-G-C
• chr9-134544468-G-T

Variant summary

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

The ENST00000435284.2(ENSG00000228877):​n.104-452G>A 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 0.305 in 152,160 control chromosomes in the GnomAD database, including 7,277 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 (7277 hom., cov: 33)
• Consequence: ENST00000435284.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506532	XR_930417.3	n.352-452G>A		intron_variant, non_coding_transcript_variant
LOC100506532	XR_109854.6	n.2233-452G>A		intron_variant, non_coding_transcript_variant
LOC100506532	XR_930416.3	n.181-452G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435284.2	n.104-452G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46329 AN: 152042 Hom.: 7271 Cov.: 33

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.305 AC: 46370 AN: 152160 Hom.: 7277 Cov.: 33 AF XY: 0.304 AC XY: 22626 AN XY: 74390

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.332

Alfa AF: 0.299 Hom.: 7024

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.61
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3118515; hg19: chr9-137436314;