rs10197851

Variant names:

• chr2-10345283-A-G
• rs10197851
• NM_002149.4:c.-111+42106A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-10345283-A-G
• chr2-10345283-A-T

Variant summary

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

The NM_002149.4(HPCAL1):​c.-111+42106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,838 control chromosomes in the GnomAD database, including 21,733 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 0.51 (21733 hom., cov: 30)
• Consequence: HPCAL1 NM_002149.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 6 publications found

Genes affected

HPCAL1 (HGNC:5145): (hippocalcin like 1) The protein encoded by this gene is a member of neuron-specific calcium-binding proteins family found in the retina and brain. It is highly similar to human hippocalcin protein and nearly identical to the rat and mouse hippocalcin like-1 proteins. It may be involved in the calcium-dependent regulation of rhodopsin phosphorylation and may be of relevance for neuronal signalling in the central nervous system. Several alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2012]

ENSG00000298642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002149.4. 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
	HPCAL1	NM_002149.4	MANE Select	c.-111+42106A>G		intron	N/A	NP_002140.2
	HPCAL1	NM_001258357.2		c.-111+15073A>G		intron	N/A	NP_001245286.1	P37235
	HPCAL1	NM_134421.3		c.-284+41341A>G		intron	N/A	NP_602293.1	Q6FGY1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HPCAL1	ENST00000307845.8	TSL:1 MANE Select	c.-111+42106A>G		intron	N/A	ENSP00000310749.3	P37235
	HPCAL1	ENST00000419810.6	TSL:1	n.-449-8933A>G		intron	N/A	ENSP00000416359.2	E9PC71
	HPCAL1	ENST00000904548.1		c.-111+42106A>G		intron	N/A	ENSP00000574607.1

Frequencies

GnomAD3 genomes AF: 0.512 AC: 77701 AN: 151720 Hom.: 21686 Cov.: 30

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.472

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.513 AC: 77821 AN: 151838 Hom.: 21733 Cov.: 30 AF XY: 0.506 AC XY: 37573 AN XY: 74194

African (AFR) AF: 0.750 AC: 31031 AN: 41402

American (AMR) AF: 0.363 AC: 5529 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1344 AN: 3472

East Asian (EAS) AF: 0.209 AC: 1078 AN: 5158

South Asian (SAS) AF: 0.570 AC: 2747 AN: 4820

European-Finnish (FIN) AF: 0.420 AC: 4414 AN: 10516

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30196 AN: 67906

Other (OTH) AF: 0.473 AC: 999 AN: 2110

Alfa AF: 0.460 Hom.: 32058

Bravo AF: 0.512

Asia WGS AF: 0.418 AC: 1455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.2
DANN	Benign	0.44
PhyloP100		-2.4
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: rs10197851; hg19: chr2-10485409;