16-51644352-T-C

Position:

• chr16-51644352-T-C

Variant summary

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

The ENST00000565308.3(HNRNPA1L3):​c.-487-979T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,644 control chromosomes in the GnomAD database, including 15,554 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 0.41 (15554 hom., cov: 30)
• Consequence: HNRNPA1L3 ENST00000565308.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HNRNPA1L3	ENST00000565308.3	c.-487-979T>C		intron_variant		6		ENSP00000493805.2

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61312 AN: 151524 Hom.: 15501 Cov.: 30

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.405 AC: 61416 AN: 151644 Hom.: 15554 Cov.: 30 AF XY: 0.400 AC XY: 29608 AN XY: 74084

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.359

Alfa AF: 0.278 Hom.: 3716

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.028
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7204626; hg19: chr16-51678263;