Genetic Variant HS1BP3:c.*935T>C (chr2-20618052-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022460.4(HS1BP3):c.*935T>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 0.0567 in 152,530 control chromosomes in the GnomAD database, including 252 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 0.057 ( 252 hom., cov: 33)

Exomes 𝑓: 0.056 ( 0 hom. )

Consequence

HS1BP3
NM_022460.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.87

Variant links:

Genes affected

HS1BP3 (HGNC:24979): (HCLS1 binding protein 3) The protein encoded by this gene shares similarity with mouse Hs1bp3, an Hcls1/Hs1-interacting protein that may be involved in lymphocyte activation. [provided by RefSeq, Jul 2008]

HS1BP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
HS1BP3	NM_022460.4 link	c.*935T>C	3_prime_UTR_variant	Exon 7 of 7	ENST00000304031.8	NP_071905.3	Q53T59Q9H7U7
HS1BP3	XM_017004696.3 link	c.920+5844T>C	intron_variant	Intron 6 of 7		XP_016860185.1
HS1BP3	XM_017004697.3 link	c.920+5844T>C	intron_variant	Intron 6 of 7		XP_016860186.1
HS1BP3	XM_017004698.2 link	c.920+5844T>C	intron_variant	Intron 6 of 7		XP_016860187.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HS1BP3	ENST00000304031 link	c.*935T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_022460.4	ENSP00000305193.3		Q53T59

Frequencies

GnomAD3 genomes

AF:

0.0567

AC:

8636

AN:

152178

Hom.:

253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0733

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.0414

Gnomad ASJ

AF:

0.0646

Gnomad EAS

AF:

0.00367

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.0432

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0587

Gnomad OTH

AF:

0.0483

GnomAD4 exome

AF:

0.0556

AC:

AN:

234

Hom.:

Cov.:

AF XY:

0.0347

AC XY:

AN XY:

144

show subpopulations

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0513

Gnomad4 NFE exome

AF:

0.0781

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0567

AC:

8639

AN:

152296

Hom.:

252

Cov.:

AF XY:

0.0540

AC XY:

4019

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.0733

Gnomad4 AMR

AF:

0.0414

Gnomad4 ASJ

AF:

0.0646

Gnomad4 EAS

AF:

0.00368

Gnomad4 SAS

AF:

0.0143

Gnomad4 FIN

AF:

0.0432

Gnomad4 NFE

AF:

0.0587

Gnomad4 OTH

AF:

0.0478

Alfa

AF:

0.0449

Hom.:

Bravo

AF:

0.0575

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.60

DANN

Benign

0.47

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over