rs1027643

chr5-92558085-C-T

Variant summary

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

The XR_001742809.2(LOC105379082):n.2166G>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 0.181 in 152,016 control chromosomes in the GnomAD database, including 5,484 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 0.18 (5484 hom., cov: 32)
• Consequence: LOC105379082 XR_001742809.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808

Genes affected

LOC105379082 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379082	XR_001742809.2	n.2166G>A		non_coding_transcript_exon_variant	3/3
LOC105379082	XR_001742810.2	n.2346G>A		non_coding_transcript_exon_variant	4/4
LOC105379082	XR_948566.3	n.2311G>A		non_coding_transcript_exon_variant	4/4
LOC105379082	XR_948568.3	n.2314G>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000512210.5	n.287+1714G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000512284.1	n.235+1714G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000513779.1	n.135-50620G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27381 AN: 151896 Hom.: 5463 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.0712

Gnomad EAS AF: 0.0760

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.0498

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.181 AC: 27452 AN: 152016 Hom.: 5484 Cov.: 32 AF XY: 0.176 AC XY: 13110 AN XY: 74300

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.0869

Gnomad4 ASJ AF: 0.0712

Gnomad4 EAS AF: 0.0754

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0498

Gnomad4 OTH AF: 0.138

Alfa AF: 0.0705 Hom.: 1882

Bravo AF: 0.196

Asia WGS AF: 0.177 AC: 614 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.34
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1027643; hg19: chr5-91893792;