rs3087692

Positions:

• chr19-4785315-G-A
• chr19-4785315-G-T

Variant summary

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

The ENST00000598782.2(ENSG00000268536):​n.334C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,206 control chromosomes in the GnomAD database, including 2,342 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 0.17 (2341 hom., cov: 32)
  • Exomes 𝑓: 0.051 (1 hom.)
• Consequence: ENST00000598782.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904620	XR_007067103.1	n.308C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598782.2	n.334C>T		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25802 AN: 152012 Hom.: 2337 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.163

GnomAD4 exome AF: 0.0513 AC: 4 AN: 78 Hom.: 1 Cov.: 0 AF XY: 0.0741 AC XY: 4 AN XY: 54

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0588

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.170 AC: 25824 AN: 152128 Hom.: 2341 Cov.: 32 AF XY: 0.168 AC XY: 12495 AN XY: 74368

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0389

Gnomad4 SAS AF: 0.0500

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.161

Alfa AF: 0.167 Hom.: 2824

Bravo AF: 0.164

Asia WGS AF: 0.0460 AC: 161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3087692; hg19: chr19-4785327;