rs16891725

chr6-26478922-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC285819 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285819	NR_038992.1	n.237G>A		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.1000-74265C>T		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-53783C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0514

Gnomad4 ASJ AF: 0.0384

Gnomad4 EAS AF: 0.0989

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0776

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0877

Alfa AF: 0.105 Hom.: 1220

Bravo AF: 0.106

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.10
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16891725; hg19: chr6-26479150;