rs3829210

Positions:

• chr8-131041906-G-A

Variant summary

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

The XR_007061183.1(LOC105375760):​n.89+2296G>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 0.445 in 152,178 control chromosomes in the GnomAD database, including 15,737 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 0.44 (15732 hom., cov: 34)
  • Exomes 𝑓: 0.47 (5 hom.)
• Consequence: LOC105375760 XR_007061183.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

LOC105375760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375760	XR_007061183.1	n.89+2296G>A		intron_variant, non_coding_transcript_variant
LOC105375760	XR_007061182.1	n.89+2296G>A		intron_variant, non_coding_transcript_variant
LOC105375760	XR_928653.3	n.81+2296G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67651 AN: 152024 Hom.: 15733 Cov.: 34

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.472 AC: 17 AN: 36 Hom.: 5 Cov.: 0 AF XY: 0.500 AC XY: 14 AN XY: 28

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.467

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.445 AC: 67671 AN: 152142 Hom.: 15732 Cov.: 34 AF XY: 0.452 AC XY: 33635 AN XY: 74360

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.450

Alfa AF: 0.492 Hom.: 23061

Bravo AF: 0.432

Asia WGS AF: 0.570 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.8
DANN	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3829210; hg19: chr8-132054152;