rs283610

chr5-73952687-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_001742745.1(LOC105379034):n.1400+5190A>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 0.42 in 152,092 control chromosomes in the GnomAD database, including 13,460 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 0.42 (13460 hom., cov: 33)
• Consequence: LOC105379034 XR_001742745.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12

Genes affected

LOC105379034 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379034	XR_001742745.1	n.1400+5190A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63821 AN: 151974 Hom.: 13441 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.420 AC: 63878 AN: 152092 Hom.: 13460 Cov.: 33 AF XY: 0.420 AC XY: 31206 AN XY: 74376

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.395

Alfa AF: 0.421 Hom.: 22129

Bravo AF: 0.416

Asia WGS AF: 0.447 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
Cadd	Benign	18
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs283610; hg19: chr5-73248512;