rs2569747

Variant names:

• chr19-50837807-A-G
• rs2569747
• ENST00000598079.1:n.213+6514A>G

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.213+6514A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,686 control chromosomes in the GnomAD database, including 12,355 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 0.40 (12355 hom., cov: 31)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.213+6514A>G		intron_variant	Intron 2 of 2
LOC105372441	NR_131205.1	n.230+6514A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.213+6514A>G		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.402 AC: 60908 AN: 151576 Hom.: 12353 Cov.: 31

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.402 AC: 60946 AN: 151686 Hom.: 12355 Cov.: 31 AF XY: 0.405 AC XY: 30041 AN XY: 74106

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.400

Alfa AF: 0.415 Hom.: 4215

Bravo AF: 0.386

Asia WGS AF: 0.393 AC: 1367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569747; hg19: chr19-51341063;