rs995834

chr19-28375689-G-A

Variant summary

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

The ENST00000592311.5(ENSG00000267320):n.167-313C>T 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 0.618 in 151,998 control chromosomes in the GnomAD database, including 31,035 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 0.62 (31035 hom., cov: 32)
• Consequence: ENST00000592311.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.393

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 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
	ENST00000592311.5	n.167-313C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000587140.5	n.193-313C>T		intron_variant, non_coding_transcript_variant		5
	ENST00000591926.1	n.160-313C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93939 AN: 151880 Hom.: 31027 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.618 AC: 93962 AN: 151998 Hom.: 31035 Cov.: 32 AF XY: 0.622 AC XY: 46225 AN XY: 74316

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.637

Alfa AF: 0.711 Hom.: 64123

Bravo AF: 0.594

Asia WGS AF: 0.533 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.43
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs995834; hg19: chr19-28866596;