rs1989486

chr19-53697365-G-A

Variant summary

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

The ENST00000710708.1(ENSG00000269842):n.462+6959G>A 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 0.554 in 151,960 control chromosomes in the GnomAD database, including 25,308 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 0.55 (25308 hom., cov: 32)
• Consequence: ENST00000710708.1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000710708.1	n.462+6959G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84090 AN: 151842 Hom.: 25261 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.554 AC: 84204 AN: 151960 Hom.: 25308 Cov.: 32 AF XY: 0.554 AC XY: 41135 AN XY: 74268

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.519

Alfa AF: 0.510 Hom.: 2612

Bravo AF: 0.567

Asia WGS AF: 0.655 AC: 2277 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	0.93
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1989486; hg19: chr19-54200619;