rs584747

chr6-49799877-A-G

Variant summary

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

The ENST00000653295.1(ENSG00000235122):n.340-17514A>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 0.136 in 152,234 control chromosomes in the GnomAD database, including 1,556 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 0.14 (1556 hom., cov: 33)
• Consequence: ENST00000653295.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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
	ENST00000653295.1	n.340-17514A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20701 AN: 152116 Hom.: 1555 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0869

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.136 AC: 20725 AN: 152234 Hom.: 1556 Cov.: 33 AF XY: 0.136 AC XY: 10112 AN XY: 74434

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0867

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.127

Alfa AF: 0.134 Hom.: 166

Bravo AF: 0.136

Asia WGS AF: 0.151 AC: 526 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.1
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: rs584747; hg19: chr6-49767590;