rs590856

Positions:

• chr6-139523292-G-A
• chr6-139523292-G-T

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+36677G>A 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 0.498 in 152,052 control chromosomes in the GnomAD database, including 19,581 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 0.50 (19581 hom., cov: 32)
• Consequence: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 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
	ENST00000647815.1	n.134+36677G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75605 AN: 151934 Hom.: 19563 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.498 AC: 75658 AN: 152052 Hom.: 19581 Cov.: 32 AF XY: 0.500 AC XY: 37188 AN XY: 74314

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.523

Alfa AF: 0.535 Hom.: 6889

Bravo AF: 0.497

Asia WGS AF: 0.509 AC: 1773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs590856; hg19: chr6-139844429;