rs1876511

chr8-10021773-A-Cchr8-10021773-A-T

Variant summary

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

The ENST00000659604.1(ENSG00000286622):n.117-31076T>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 0.145 in 152,214 control chromosomes in the GnomAD database, including 2,222 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 0.15 (2222 hom., cov: 33)
• Consequence: ENST00000659604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659604.1	n.117-31076T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22111 AN: 152096 Hom.: 2226 Cov.: 33

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.145 AC: 22103 AN: 152214 Hom.: 2222 Cov.: 33 AF XY: 0.155 AC XY: 11560 AN XY: 74418

Gnomad4 AFR AF: 0.0456

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.151

Alfa AF: 0.130 Hom.: 526

Bravo AF: 0.143

Asia WGS AF: 0.320 AC: 1108 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	4.9
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876511; hg19: chr8-9879283;