16-51644352-T-C

Variant names:

• chr16-51644352-T-C
• rs7204626
• ENST00000565308.3:c.-487-979T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565308.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HNRNPA1L3	ENST00000565308.3	TSL:6	c.-487-979T>C		intron	N/A	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

African (AFR) AF: 0.730 AC: 30114 AN: 41254

American (AMR) AF: 0.328 AC: 4988 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1257 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1470 AN: 5140

South Asian (SAS) AF: 0.293 AC: 1404 AN: 4794

European-Finnish (FIN) AF: 0.248 AC: 2613 AN: 10532

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18532 AN: 67920

Other (OTH) AF: 0.359 AC: 757 AN: 2106

Alfa AF: 0.284 Hom.: 4316

Bravo AF: 0.424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.028
DANN	Benign	0.45
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs7204626; hg19: chr16-51678263;