rs6904596

Positions:

• chr6-27523520-G-A

Variant summary

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

The ENST00000401954.2(HNRNPA1P1):​n.125G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0966 in 1,428,582 control chromosomes in the GnomAD database, including 8,285 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 0.11 (1087 hom., cov: 31)
  • Exomes 𝑓: 0.095 (7198 hom.)
• Consequence: HNRNPA1P1 ENST00000401954.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.00

Genes affected

HNRNPA1P1 (HGNC:13957): (heterogeneous nuclear ribonucleoprotein A1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 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
HNRNPA1P1	ENST00000401954.2	n.125G>A		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16137 AN: 152006 Hom.: 1088 Cov.: 31

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.0872

GnomAD4 exome AF: 0.0955 AC: 121838 AN: 1276458 Hom.: 7198 Cov.: 20 AF XY: 0.0913 AC XY: 58669 AN XY: 642924

Gnomad4 AFR exome AF: 0.181

Gnomad4 AMR exome AF: 0.0464

Gnomad4 ASJ exome AF: 0.0335

Gnomad4 EAS exome AF: 0.000130

Gnomad4 SAS exome AF: 0.00319

Gnomad4 FIN exome AF: 0.0433

Gnomad4 NFE exome AF: 0.111

Gnomad4 OTH exome AF: 0.0873

GnomAD4 genome AF: 0.106 AC: 16144 AN: 152124 Hom.: 1087 Cov.: 31 AF XY: 0.0987 AC XY: 7343 AN XY: 74402

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0663

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00207

Gnomad4 FIN AF: 0.0396

Gnomad4 NFE AF: 0.0986

Gnomad4 OTH AF: 0.0863

Alfa AF: 0.0923 Hom.: 1040

Bravo AF: 0.113

Asia WGS AF: 0.0120 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	1.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6904596; hg19: chr6-27491299;