rs2431664

Positions:

• chr5-172776908-G-A

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.70-584G>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 0.109 in 152,114 control chromosomes in the GnomAD database, including 1,177 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 0.11 (1177 hom., cov: 31)
• Consequence: ENST00000523005.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377730	XR_941232.3	n.1130-584G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000523005.1	n.70-584G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000652842.1	n.200G>A		non_coding_transcript_exon_variant	1/2
	ENST00000650258.1	n.86+358G>A		intron_variant, non_coding_transcript_variant
	ENST00000687811.1	n.256-584G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16502 AN: 151996 Hom.: 1174 Cov.: 31

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0969

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.109 AC: 16515 AN: 152114 Hom.: 1177 Cov.: 31 AF XY: 0.106 AC XY: 7882 AN XY: 74362

Gnomad4 AFR AF: 0.0394

Gnomad4 AMR AF: 0.0968

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.00329

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.120

Alfa AF: 0.140 Hom.: 764

Bravo AF: 0.104

Asia WGS AF: 0.0660 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2431664; hg19: chr5-172203911;