rs34734159

Variant names:

• chr5-179616981-C-CA
• rs34734159
• NM_001257293.2:c.1118-24dupT

Your query was ambiguous. Multiple possible variants found:

• chr5-179616981-C-CA
• chr5-179616981-C-CAA

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001257293.2(HNRNPH1):​c.1118-24dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000897 in 1,114,964 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 9.0e-7 (0 hom.)
• Consequence: HNRNPH1 NM_001257293.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.21

Genes affected

HNRNPH1 (HGNC:5041): (heterogeneous nuclear ribonucleoprotein H1) This gene encodes a member of a subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA binding proteins that complex with heterogeneous nuclear RNA. These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some may shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has three repeats of quasi-RRM domains that bind to RNA and is very similar to the family member HNRPF. This gene may be associated with hereditary lymphedema type I. Alternatively spliced transcript variants have been described [provided by RefSeq, Mar 2012]

LOC128966623 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HNRNPH1	NM_001257293.2	c.1118-24dupT		intron_variant	Intron 10 of 13	ENST00000393432.9	NP_001244222.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPH1	ENST00000393432.9	c.1118-24dupT		intron_variant	Intron 10 of 13	1	NM_001257293.2	ENSP00000377082.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 8.97e-7 AC: 1 AN: 1114964 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 565632

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 29062

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 42468

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 23870

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 39038

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 80032

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 51578

Gnomad4 NFE exome AF: 0.00000126 AC: 1 AN: 793554

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 50104

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs34734159; hg19: chr5-179043982;