rs2857708

Positions:

• chr6-31565829-C-T

Variant summary

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

The NR_149045.1(LOC100287329):​n.122-5107G>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 0.104 in 152,114 control chromosomes in the GnomAD database, including 959 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 0.10 (959 hom., cov: 31)
• Consequence: LOC100287329 NR_149045.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100287329	NR_149045.1	n.122-5107G>A		intron_variant, non_coding_transcript_variant
LTA	XM_047418773.1	c.-342+4560C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691266.1	n.119-5107G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15835 AN: 151996 Hom.: 961 Cov.: 31

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.0826

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.104 AC: 15837 AN: 152114 Hom.: 959 Cov.: 31 AF XY: 0.103 AC XY: 7695 AN XY: 74358

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.0825

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.114

Alfa AF: 0.127 Hom.: 1210

Bravo AF: 0.101

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2857708; hg19: chr6-31533606;