rs2659053

Positions:

• chr19-50837538-G-A

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.213+6245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151,898 control chromosomes in the GnomAD database, including 15,092 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 0.44 (15092 hom., cov: 31)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.213+6245G>A		intron_variant
LOC105372441	NR_131205.1	n.230+6245G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.213+6245G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66823 AN: 151780 Hom.: 15075 Cov.: 31

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.440 AC: 66888 AN: 151898 Hom.: 15092 Cov.: 31 AF XY: 0.441 AC XY: 32732 AN XY: 74238

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.429

Alfa AF: 0.405 Hom.: 17170

Bravo AF: 0.458

Asia WGS AF: 0.533 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2659053; hg19: chr19-51340794;