rs545854

chr8-10002570-G-C

Variant summary

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

The ENST00000659604.1(ENSG00000286622):n.117-11873C>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 0.847 in 152,132 control chromosomes in the GnomAD database, including 55,139 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 0.85 (55139 hom., cov: 30)
• Consequence: ENST00000659604.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 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.117-11873C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128667 AN: 152014 Hom.: 55077 Cov.: 30

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.847 AC: 128788 AN: 152132 Hom.: 55139 Cov.: 30 AF XY: 0.839 AC XY: 62368 AN XY: 74344

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.879

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.840

Alfa AF: 0.856 Hom.: 7027

Bravo AF: 0.847

Asia WGS AF: 0.671 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs545854; hg19: chr8-9860080;