rs1391727

chr16-51619446-G-C

Variant summary

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

The ENST00000565308.3(HNRNPA1L3):c.-487-25885G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,034 control chromosomes in the GnomAD database, including 4,174 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 0.13 (4174 hom., cov: 32)
• Consequence: HNRNPA1L3 ENST00000565308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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.-487-25885G>C		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20393 AN: 151918 Hom.: 4148 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0458

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00447

Gnomad OTH AF: 0.0924

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

GnomAD4 genome AF: 0.135 AC: 20472 AN: 152034 Hom.: 4174 Cov.: 32 AF XY: 0.133 AC XY: 9866 AN XY: 74368

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0458

Gnomad4 EAS AF: 0.0343

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00447

Gnomad4 OTH AF: 0.0915

Alfa AF: 0.0780 Hom.: 274

Bravo AF: 0.149

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.036
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: rs1391727; hg19: chr16-51653357;