rs2569753

chr19-50840922-T-C

Variant summary

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

The NR_131205.1(LOC105372441):n.230+9629T>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 0.471 in 152,022 control chromosomes in the GnomAD database, including 18,501 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 0.47 (18501 hom., cov: 31)
• Consequence: LOC105372441 NR_131205.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372441	NR_131205.1	n.230+9629T>C		intron_variant, non_coding_transcript_variant
LOC105372441	NR_131203.1	n.213+9629T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598079.1	n.213+9629T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71587 AN: 151902 Hom.: 18498 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.574

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.471 AC: 71599 AN: 152022 Hom.: 18501 Cov.: 31 AF XY: 0.470 AC XY: 34904 AN XY: 74298

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.360

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.504

Alfa AF: 0.518 Hom.: 2643

Bravo AF: 0.445

Asia WGS AF: 0.436 AC: 1518 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	0.61
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2569753; hg19: chr19-51344178;