rs3743832

chr16-9120023-A-Cchr16-9120023-A-T

Variant summary

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

The NM_014117.3(HAPSTR1):c.*3111A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,044 control chromosomes in the GnomAD database, including 22,933 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 0.55 (22933 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: HAPSTR1 NM_014117.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

HAPSTR1 (HGNC:30103): (HUWE1 associated protein modifying stress responses)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HAPSTR1	NM_014117.3	c.*3111A>C		3_prime_UTR_variant	4/4	ENST00000327827.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAPSTR1	ENST00000327827.12	c.*3111A>C		3_prime_UTR_variant	4/4	1	NM_014117.3	P1

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82885 AN: 151924 Hom.: 22913 Cov.: 32

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.531

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.545 AC: 82930 AN: 152042 Hom.: 22933 Cov.: 32 AF XY: 0.545 AC XY: 40499 AN XY: 74314

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.530

Alfa AF: 0.565 Hom.: 10128

Bravo AF: 0.534

Asia WGS AF: 0.459 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.0
Dann	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3743832; hg19: chr16-9213880;