rs4877280

Positions:

• chr9-84571490-G-A

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.979-11707G>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 0.325 in 152,114 control chromosomes in the GnomAD database, including 8,753 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 0.33 (8753 hom., cov: 33)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724036	XR_007061623.1	n.6210-2986G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650453.1	n.979-11707G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49403 AN: 151996 Hom.: 8720 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.325 AC: 49500 AN: 152114 Hom.: 8753 Cov.: 33 AF XY: 0.328 AC XY: 24378 AN XY: 74376

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.310

Alfa AF: 0.302 Hom.: 1271

Bravo AF: 0.338

Asia WGS AF: 0.451 AC: 1563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.44
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4877280; hg19: chr9-87186405;