rs282381

Positions:

• chr5-73981548-G-A
• chr5-73981548-G-C

Variant summary

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

The XR_001742745.1(LOC105379034):​n.1598-817G>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 0.603 in 152,140 control chromosomes in the GnomAD database, including 28,475 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 0.60 (28475 hom., cov: 33)
• Consequence: LOC105379034 XR_001742745.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

LOC105379034 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379034	XR_001742745.1	n.1598-817G>A		intron_variant, non_coding_transcript_variant
LOC105379034	XR_001742746.1	n.340-817G>A		intron_variant, non_coding_transcript_variant
LOC105379034	XR_007058819.1	n.262-817G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91681 AN: 152022 Hom.: 28416 Cov.: 33

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.603 AC: 91802 AN: 152140 Hom.: 28475 Cov.: 33 AF XY: 0.606 AC XY: 45085 AN XY: 74370

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.573

Alfa AF: 0.535 Hom.: 28363

Bravo AF: 0.613

Asia WGS AF: 0.748 AC: 2599 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282381; hg19: chr5-73277373;