NR_188296.1:n.2311G>A

Variant names:

• chr5-92558085-C-T
• rs1027643
• NR_188296.1:n.2311G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188296.1(LOC105379082):​n.2311G>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 NR_188296.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808
• Publications: 19 publications found

Genes affected

LOC105379082 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105379082	NR_188296.1	n.2311G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105379082	NR_188297.1	n.2166G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105379082	NR_188298.1	n.452+1714G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249776	ENST00000512210.5	n.287+1714G>A		intron_variant	Intron 2 of 3	3
ENSG00000249776	ENST00000512284.2	n.449+1714G>A		intron_variant	Intron 2 of 2	3
ENSG00000249776	ENST00000513779.1	n.135-50620G>A		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.499 AC: 20678 AN: 41402

American (AMR) AF: 0.0869 AC: 1327 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0712 AC: 247 AN: 3470

East Asian (EAS) AF: 0.0754 AC: 390 AN: 5172

South Asian (SAS) AF: 0.137 AC: 663 AN: 4824

European-Finnish (FIN) AF: 0.0361 AC: 383 AN: 10600

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0498 AC: 3382 AN: 67964

Other (OTH) AF: 0.138 AC: 292 AN: 2116

Alfa AF: 0.0895 Hom.: 7441

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1027643; hg19: chr5-91893792;