rs4678180

Variant names:

• chr3-122318950-T-C
• rs4678180
• ENST00000491091.1:n.*209T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000491091.1(HNRNPA1P23):​n.*209T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,992 control chromosomes in the GnomAD database, including 30,475 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 0.62 (30475 hom., cov: 32)
• Consequence: HNRNPA1P23 ENST00000491091.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64
• Publications: 5 publications found

Genes affected

HNRNPA1P23 (HGNC:39541): (heterogeneous nuclear ribonucleoprotein A1 pseudogene 23)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HNRNPA1P23	ENST00000491091.1	n.*209T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94824 AN: 151874 Hom.: 30473 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.624 AC: 94847 AN: 151992 Hom.: 30475 Cov.: 32 AF XY: 0.622 AC XY: 46184 AN XY: 74274

African (AFR) AF: 0.483 AC: 20019 AN: 41422

American (AMR) AF: 0.613 AC: 9364 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2700 AN: 5164

South Asian (SAS) AF: 0.536 AC: 2584 AN: 4820

European-Finnish (FIN) AF: 0.674 AC: 7115 AN: 10554

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48593 AN: 67976

Other (OTH) AF: 0.635 AC: 1338 AN: 2108

Alfa AF: 0.657 Hom.: 5599

Bravo AF: 0.618

Asia WGS AF: 0.485 AC: 1688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.5
DANN	Benign	0.76
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs4678180; hg19: chr3-122037797;