rs2595613

Positions:

• chr8-92567026-C-A

Variant summary

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

The NR_125827.1(LOC102724710):​n.460-1456G>T 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 0.116 in 152,084 control chromosomes in the GnomAD database, including 1,694 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 0.12 (1694 hom., cov: 32)
• Consequence: LOC102724710 NR_125827.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724710	NR_125827.1	n.460-1456G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648652.1	n.534+1977G>T		intron_variant, non_coding_transcript_variant
	ENST00000523284.2	n.542-1456G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000653143.1	n.546-1456G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17603 AN: 151966 Hom.: 1695 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0463

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0522

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.116 AC: 17617 AN: 152084 Hom.: 1694 Cov.: 32 AF XY: 0.115 AC XY: 8531 AN XY: 74356

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0522

Gnomad4 OTH AF: 0.118

Alfa AF: 0.109 Hom.: 266

Bravo AF: 0.131

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2595613; hg19: chr8-93579254;