rs3181224

chr5-159313842-A-G

Variant summary

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

The XR_941138.3(LOC105377683):n.401-1376A>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 0.101 in 152,282 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 32)
• Consequence: LOC105377683 XR_941138.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

Genes affected

LOC105377683 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377683	XR_941138.3	n.401-1376A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521472.6	n.289+2428A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15444 AN: 152162 Hom.: 838 Cov.: 32

Gnomad AFR AF: 0.0851

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0712

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.101 AC: 15456 AN: 152282 Hom.: 842 Cov.: 32 AF XY: 0.0988 AC XY: 7355 AN XY: 74454

Gnomad4 AFR AF: 0.0850

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0405

Gnomad4 SAS AF: 0.0640

Gnomad4 FIN AF: 0.0712

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.118

Alfa AF: 0.118 Hom.: 1582

Bravo AF: 0.109

Asia WGS AF: 0.0610 AC: 211 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.43
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181224; hg19: chr5-158740850;