chr2-20618052-A-G

Variant names:

• chr2-20618052-A-G
• rs1047163
• NM_022460.4:c.*935T>C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0711 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS1BP3	NM_022460.4	MANE Select	c.*935T>C		3_prime_UTR	Exon 7 of 7	NP_071905.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HS1BP3	ENST00000304031.8	TSL:1 MANE Select	c.*935T>C		3_prime_UTR	Exon 7 of 7	ENSP00000305193.3	Q53T59
	HS1BP3	ENST00000897119.1		c.*935T>C		3_prime_UTR	Exon 8 of 8	ENSP00000567178.1
	HS1BP3	ENST00000897121.1		c.*935T>C		3_prime_UTR	Exon 8 of 8	ENSP00000567180.1

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8636 AN: 152178 Hom.: 253 Cov.: 33

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: 13 AN: 234 Hom.: 0 Cov.: 0 AF XY: 0.0347 AC XY: 5 AN XY: 144

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.0513 AC: 8 AN: 156

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0781 AC: 5 AN: 64

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0567 AC: 8639 AN: 152296 Hom.: 252 Cov.: 33 AF XY: 0.0540 AC XY: 4019 AN XY: 74466

African (AFR) AF: 0.0733 AC: 3046 AN: 41578

American (AMR) AF: 0.0414 AC: 633 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.00368 AC: 19 AN: 5160

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4832

European-Finnish (FIN) AF: 0.0432 AC: 458 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0587 AC: 3994 AN: 68016

Other (OTH) AF: 0.0478 AC: 101 AN: 2112

Alfa AF: 0.0470 Hom.: 86

Bravo AF: 0.0575

Asia WGS AF: 0.0190 AC: 65 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.60
DANN	Benign	0.47
PhyloP100		-1.9
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: rs1047163; hg19: chr2-20817812;