rs3743832

Variant names:

• chr16-9120023-A-C
• rs3743832
• NM_014117.3:c.*3111A>C

Your query was ambiguous. Multiple possible variants found:

• chr16-9120023-A-C
• chr16-9120023-A-G
• chr16-9120023-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014117.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAPSTR1	NM_014117.3	MANE Select	c.*3111A>C		3_prime_UTR	Exon 4 of 4	NP_054836.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAPSTR1	ENST00000327827.12	TSL:1 MANE Select	c.*3111A>C		3_prime_UTR	Exon 4 of 4	ENSP00000331720.7	Q14CZ0-1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.454 AC: 18835 AN: 41478

American (AMR) AF: 0.576 AC: 8801 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3470

East Asian (EAS) AF: 0.421 AC: 2178 AN: 5174

South Asian (SAS) AF: 0.498 AC: 2399 AN: 4818

European-Finnish (FIN) AF: 0.634 AC: 6678 AN: 10532

Middle Eastern (MID) AF: 0.527 AC: 154 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40117 AN: 67970

Other (OTH) AF: 0.530 AC: 1119 AN: 2112

Alfa AF: 0.565 Hom.: 11524

Bravo AF: 0.534

Asia WGS AF: 0.459 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.44
PhyloP100		-0.024
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3743832; hg19: chr16-9213880;