NR_038992.1:n.237G>A

Variant names:

• chr6-26478922-C-T
• rs16891725
• NR_038992.1:n.237G>A

Variant summary

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

The NR_038992.1(LOC285819):​n.237G>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 0.108 in 151,952 control chromosomes in the GnomAD database, including 943 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 (943 hom., cov: 32)
• Consequence: LOC285819 NR_038992.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 28 publications found

Genes affected

LOC285819 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_038992.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC285819	NR_038992.1		n.237G>A		non_coding_transcript_exon	Exon 2 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291336	ENST00000707189.1		n.1000-74265C>T		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1001-53783C>T		intron	N/A
	ENSG00000300236	ENST00000770281.1		n.559-6729G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16408 AN: 151836 Hom.: 943 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.0987

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0776

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.108 AC: 16418 AN: 151952 Hom.: 943 Cov.: 32 AF XY: 0.104 AC XY: 7743 AN XY: 74276

African (AFR) AF: 0.135 AC: 5580 AN: 41408

American (AMR) AF: 0.0514 AC: 786 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3466

East Asian (EAS) AF: 0.0989 AC: 512 AN: 5176

South Asian (SAS) AF: 0.117 AC: 560 AN: 4806

European-Finnish (FIN) AF: 0.0776 AC: 819 AN: 10548

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7637 AN: 67956

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.110 Hom.: 3165

Bravo AF: 0.106

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.10
DANN	Benign	0.27
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs16891725; hg19: chr6-26479150;