rs1531517

Variant names:

• chr19-44738916-G-A
• rs1531517
• ENST00000693032.3:n.1340G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693032.3(ENSG00000288773):​n.1340G>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: ENSG00000288773 ENST00000693032.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.56
• Publications: 36 publications found

Genes affected

ENSG00000288773 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288773	ENST00000693032.3	n.1340G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000288773	ENST00000790574.1	n.783G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000288773	ENST00000790564.1	n.156+1074G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.218 AC: 9033 AN: 41514

American (AMR) AF: 0.0635 AC: 971 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 364 AN: 3466

East Asian (EAS) AF: 0.157 AC: 808 AN: 5156

South Asian (SAS) AF: 0.173 AC: 833 AN: 4826

European-Finnish (FIN) AF: 0.0518 AC: 550 AN: 10612

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0652 AC: 4433 AN: 67970

Other (OTH) AF: 0.0932 AC: 197 AN: 2114

Alfa AF: 0.0816 Hom.: 1118

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
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs1531517; hg19: chr19-45242173;