ENST00000565308.3:c.-488+22479G>A

Variant names:

• chr16-51576036-G-A
• rs2030114
• ENST00000565308.3:c.-488+22479G>A

Variant summary

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

The ENST00000565308.3(HNRNPA1L3):​c.-488+22479G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 148,650 control chromosomes in the GnomAD database, including 4,664 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 0.22 (4664 hom., cov: 30)
• Consequence: HNRNPA1L3 ENST00000565308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 3 publications found

Genes affected

HNRNPA1L3 (HGNC:48778): (heterogeneous nuclear ribonucleoprotein A1 like 3) Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing and mRNA processing. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 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
HNRNPA1L3	ENST00000565308.3	c.-488+22479G>A		intron_variant	Intron 1 of 1	6		ENSP00000493805.2

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33305 AN: 148548 Hom.: 4654 Cov.: 30

Gnomad AFR AF: 0.373

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.211

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.224 AC: 33348 AN: 148650 Hom.: 4664 Cov.: 30 AF XY: 0.220 AC XY: 15913 AN XY: 72334

African (AFR) AF: 0.373 AC: 14954 AN: 40072

American (AMR) AF: 0.166 AC: 2486 AN: 14964

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1015 AN: 3442

East Asian (EAS) AF: 0.00464 AC: 24 AN: 5176

South Asian (SAS) AF: 0.153 AC: 722 AN: 4724

European-Finnish (FIN) AF: 0.153 AC: 1505 AN: 9860

Middle Eastern (MID) AF: 0.220 AC: 63 AN: 286

European-Non Finnish (NFE) AF: 0.180 AC: 12108 AN: 67154

Other (OTH) AF: 0.194 AC: 399 AN: 2062

Alfa AF: 0.200 Hom.: 6065

Bravo AF: 0.234

Asia WGS AF: 0.0750 AC: 261 AN: 3384

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.48
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2030114; hg19: chr16-51609947;