rs4471448

chr11-87372282-A-G

Variant summary

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

The XR_002957260.2(LOC107984361):n.319-510A>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 0.301 in 152,090 control chromosomes in the GnomAD database, including 8,195 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 (8195 hom., cov: 32)
• Consequence: LOC107984361 XR_002957260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260

Genes affected

LOC107984361 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984361	XR_002957260.2	n.319-510A>G		intron_variant, non_coding_transcript_variant
LOC107984361	XR_001748316.2	n.318+9806A>G		intron_variant, non_coding_transcript_variant
LOC107984361	XR_002957261.2	n.318+9806A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45746 AN: 151972 Hom.: 8202 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.301 AC: 45726 AN: 152090 Hom.: 8195 Cov.: 32 AF XY: 0.295 AC XY: 21944 AN XY: 74332

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.339

Alfa AF: 0.391 Hom.: 23983

Bravo AF: 0.293

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4471448; hg19: chr11-87083324;