5-172771552-G-A

Position:

• chr5-172771552-G-A

Variant summary

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

The XR_941232.3(LOC105377730):​n.194G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,128 control chromosomes in the GnomAD database, including 3,865 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 0.22 (3865 hom., cov: 33)
• Consequence: LOC105377730 XR_941232.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

Genes affected

LOC105377730 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377730	XR_941232.3	n.194G>A		non_coding_transcript_exon_variant	1/2
LOC105377730	XR_941233.3	n.194G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000523005.1	n.70-5940G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33742 AN: 152012 Hom.: 3866 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.222 AC: 33742 AN: 152128 Hom.: 3865 Cov.: 33 AF XY: 0.220 AC XY: 16345 AN XY: 74386

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.181

Alfa AF: 0.167 Hom.: 432

Bravo AF: 0.212

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881152; hg19: chr5-172198555;