rs6904596

Variant names:

• chr6-27523520-G-A
• rs6904596
• ENST00000401954.2:n.125G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 37 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HNRNPA1P1		n.27523520G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPA1P1	ENST00000401954.2	n.125G>A		non_coding_transcript_exon_variant	Exon 2 of 2	6

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

African (AFR) AF: 0.181 AC: 5409 AN: 29940

American (AMR) AF: 0.0464 AC: 2031 AN: 43742

Ashkenazi Jewish (ASJ) AF: 0.0335 AC: 823 AN: 24590

East Asian (EAS) AF: 0.000130 AC: 5 AN: 38578

South Asian (SAS) AF: 0.00319 AC: 263 AN: 82392

European-Finnish (FIN) AF: 0.0433 AC: 1600 AN: 36962

Middle Eastern (MID) AF: 0.0272 AC: 104 AN: 3826

European-Non Finnish (NFE) AF: 0.111 AC: 106903 AN: 962618

Other (OTH) AF: 0.0873 AC: 4700 AN: 53810

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

African (AFR) AF: 0.182 AC: 7565 AN: 41456

American (AMR) AF: 0.0663 AC: 1013 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00207 AC: 10 AN: 4824

European-Finnish (FIN) AF: 0.0396 AC: 420 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0986 AC: 6703 AN: 67990

Other (OTH) AF: 0.0863 AC: 182 AN: 2110

Alfa AF: 0.102 Hom.: 2329

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
PhyloP100		4.0

Splicing

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

Other links and lift over

dbSNP: rs6904596; hg19: chr6-27491299;