2-20618791-G-C

Variant names:

• chr2-20618791-G-C
• rs11680700
• NM_022460.4:c.*196C>G

Variant summary

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

The NM_022460.4(HS1BP3):​c.*196C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 1,392,082 control chromosomes in the GnomAD database, including 1,867 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 0.037 (157 hom., cov: 33)
  • Exomes 𝑓: 0.049 (1710 hom.)
• Consequence: HS1BP3 NM_022460.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 8 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022460.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS1BP3	NM_022460.4	MANE Select	c.*196C>G		3_prime_UTR	Exon 7 of 7	NP_071905.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS1BP3	ENST00000304031.8	TSL:1 MANE Select	c.*196C>G		3_prime_UTR	Exon 7 of 7	ENSP00000305193.3
	HS1BP3	ENST00000651498.1		n.*816C>G		non_coding_transcript_exon	Exon 6 of 6	ENSP00000498575.1
	HS1BP3	ENST00000651498.1		n.*816C>G		3_prime_UTR	Exon 6 of 6	ENSP00000498575.1

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5644 AN: 152130 Hom.: 157 Cov.: 33

Gnomad AFR AF: 0.00929

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0303

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.0359

GnomAD4 exome AF: 0.0495 AC: 61346 AN: 1239834 Hom.: 1710 Cov.: 34 AF XY: 0.0494 AC XY: 29488 AN XY: 597246

African (AFR) AF: 0.00727 AC: 200 AN: 27512

American (AMR) AF: 0.0267 AC: 391 AN: 14644

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 901 AN: 17980

East Asian (EAS) AF: 0.00 AC: 0 AN: 32324

South Asian (SAS) AF: 0.00954 AC: 505 AN: 52920

European-Finnish (FIN) AF: 0.0575 AC: 1622 AN: 28192

Middle Eastern (MID) AF: 0.0166 AC: 84 AN: 5072

European-Non Finnish (NFE) AF: 0.0550 AC: 55504 AN: 1009828

Other (OTH) AF: 0.0416 AC: 2139 AN: 51362

GnomAD4 genome AF: 0.0371 AC: 5643 AN: 152248 Hom.: 157 Cov.: 33 AF XY: 0.0369 AC XY: 2751 AN XY: 74456

African (AFR) AF: 0.00926 AC: 385 AN: 41568

American (AMR) AF: 0.0303 AC: 463 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.00871 AC: 42 AN: 4824

European-Finnish (FIN) AF: 0.0675 AC: 716 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0544 AC: 3696 AN: 67986

Other (OTH) AF: 0.0355 AC: 75 AN: 2110

Alfa AF: 0.0191 Hom.: 5

Bravo AF: 0.0335

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.46
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism

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: rs11680700; hg19: chr2-20818551;