chr3-30356076-G-A

Variant names:

• chr3-30356076-G-A
• rs1495592
• ENST00000813769.1:n.506-14753C>T

Variant summary

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

The ENST00000813769.1(ENSG00000227549):​n.506-14753C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,058 control chromosomes in the GnomAD database, including 6,803 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 0.30 (6803 hom., cov: 32)
• Consequence: ENSG00000227549 ENST00000813769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.417
• Publications: 7 publications found

Genes affected

ENSG00000227549 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927995	XR_427323.4	n.1149+5137G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227549	ENST00000813769.1	n.506-14753C>T		intron_variant	Intron 5 of 5
ENSG00000289450	ENST00000813894.1	n.240+5137G>A		intron_variant	Intron 1 of 3
ENSG00000289450	ENST00000813896.1	n.222+5137G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44865 AN: 151938 Hom.: 6796 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.295 AC: 44889 AN: 152058 Hom.: 6803 Cov.: 32 AF XY: 0.295 AC XY: 21948 AN XY: 74306

African (AFR) AF: 0.293 AC: 12145 AN: 41502

American (AMR) AF: 0.405 AC: 6180 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1750 AN: 5144

South Asian (SAS) AF: 0.279 AC: 1347 AN: 4826

European-Finnish (FIN) AF: 0.285 AC: 3016 AN: 10576

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18643 AN: 67960

Other (OTH) AF: 0.280 AC: 592 AN: 2112

Alfa AF: 0.281 Hom.: 2165

Bravo AF: 0.307

Asia WGS AF: 0.333 AC: 1161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1495592; hg19: chr3-30397568;