rs1986778

chr11-87509702-G-Achr11-87509702-G-C

Variant summary

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

The XR_002957260.2(LOC107984361):n.396-43597G>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 0.432 in 151,878 control chromosomes in the GnomAD database, including 14,826 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 0.43 (14826 hom., cov: 31)
• Consequence: LOC107984361 XR_002957260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

LOC107984361 (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 = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984361	XR_002957260.2	n.396-43597G>A		intron_variant, non_coding_transcript_variant
LOC107984361	XR_001748316.2	n.319-43597G>A		intron_variant, non_coding_transcript_variant
LOC107984361	XR_002957261.2	n.319-43597G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65649 AN: 151760 Hom.: 14821 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.432 AC: 65663 AN: 151878 Hom.: 14826 Cov.: 31 AF XY: 0.430 AC XY: 31943 AN XY: 74210

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.453

Alfa AF: 0.479 Hom.: 24329

Bravo AF: 0.426

Asia WGS AF: 0.335 AC: 1166 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	0.014
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1986778; hg19: chr11-87220744;