rs2030114

chr16-51576036-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HNRNPA1L3	ENST00000565308.3	c.-488+22479G>A		intron_variant				P1

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

Gnomad4 AFR AF: 0.373

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.00464

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.194

Alfa AF: 0.203 Hom.: 649

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030114; hg19: chr16-51609947;