rs6569926

Variant names:

• chr6-134098874-G-A
• rs6569926
• ENST00000663785.1:n.350+12863G>A

Variant summary

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

The ENST00000663785.1(ENSG00000287413):​n.350+12863G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,946 control chromosomes in the GnomAD database, including 11,221 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 0.37 (11221 hom., cov: 31)
• Consequence: ENSG00000287413 ENST00000663785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 2 publications found

Genes affected

ENSG00000287413 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901404	XR_007059774.1	n.2284+12863G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287413	ENST00000663785.1	n.350+12863G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56872 AN: 151826 Hom.: 11199 Cov.: 31

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.375 AC: 56928 AN: 151946 Hom.: 11221 Cov.: 31 AF XY: 0.373 AC XY: 27722 AN XY: 74274

African (AFR) AF: 0.464 AC: 19213 AN: 41412

American (AMR) AF: 0.241 AC: 3674 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1275 AN: 3470

East Asian (EAS) AF: 0.121 AC: 628 AN: 5178

South Asian (SAS) AF: 0.371 AC: 1789 AN: 4816

European-Finnish (FIN) AF: 0.423 AC: 4462 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24708 AN: 67944

Other (OTH) AF: 0.354 AC: 747 AN: 2108

Alfa AF: 0.365 Hom.: 33526

Bravo AF: 0.362

Asia WGS AF: 0.234 AC: 818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.33
DANN	Benign	0.62
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6569926; hg19: chr6-134420012; COSMIC: COSV69427304;