rs2505059

Positions:

• chr6-98048076-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000656098.1(ENSG00000271860):​n.1316-51110A>G 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 0.517 in 151,814 control chromosomes in the GnomAD database, including 20,576 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 0.52 (20576 hom., cov: 31)
• Consequence: ENST00000656098.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000656098.1	n.1316-51110A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78436 AN: 151696 Hom.: 20545 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.517 AC: 78528 AN: 151814 Hom.: 20576 Cov.: 31 AF XY: 0.522 AC XY: 38688 AN XY: 74180

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.629

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.514

Alfa AF: 0.484 Hom.: 34449

Bravo AF: 0.509

Asia WGS AF: 0.528 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	12
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505059; hg19: chr6-98495952;