rs592423

Positions:

• chr6-139519556-A-C

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+32941A>C 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 0.499 in 152,026 control chromosomes in the GnomAD database, including 19,427 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 (19427 hom., cov: 31)
• Consequence: ENST00000647815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.651 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+32941A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75783 AN: 151908 Hom.: 19400 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.499 AC: 75847 AN: 152026 Hom.: 19427 Cov.: 31 AF XY: 0.499 AC XY: 37100 AN XY: 74322

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.520

Alfa AF: 0.542 Hom.: 20670

Bravo AF: 0.493

Asia WGS AF: 0.496 AC: 1725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs592423; hg19: chr6-139840693;