rs1531517

chr19-44738916-G-A

Variant summary

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

The ENST00000693032.2(ENSG00000288773):n.1339G>A 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 0.113 in 152,158 control chromosomes in the GnomAD database, including 1,312 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 0.11 (1312 hom., cov: 32)
• Consequence: ENST00000693032.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.56

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 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
	ENST00000693032.2	n.1339G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.113 AC: 17218 AN: 152040 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0653

Gnomad OTH AF: 0.0913

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

GnomAD4 genome AF: 0.113 AC: 17234 AN: 152158 Hom.: 1312 Cov.: 32 AF XY: 0.112 AC XY: 8302 AN XY: 74378

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0635

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0652

Gnomad4 OTH AF: 0.0932

Alfa AF: 0.0758 Hom.: 594

Bravo AF: 0.117

Asia WGS AF: 0.183 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.29
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1531517; hg19: chr19-45242173;