chr6-139523292-G-A

Variant names:

• chr6-139523292-G-A
• rs590856
• ENST00000647815.1:n.134+36677G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000647815.1(ENSG00000226571):​n.134+36677G>A variant causes a intron 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: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.805
• Publications: 24 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226571	ENST00000647815.1	n.134+36677G>A		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000775574.1	n.194-23950G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.358 AC: 14830 AN: 41472

American (AMR) AF: 0.620 AC: 9469 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2118 AN: 3472

East Asian (EAS) AF: 0.322 AC: 1665 AN: 5176

South Asian (SAS) AF: 0.671 AC: 3238 AN: 4824

European-Finnish (FIN) AF: 0.480 AC: 5066 AN: 10554

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37496 AN: 67960

Other (OTH) AF: 0.523 AC: 1105 AN: 2112

Alfa AF: 0.522 Hom.: 39756

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs590856; hg19: chr6-139844429;