rs1800642

Variant names:

• chr16-71371881-C-T
• rs1800642
• NM_001740.5:c.95-272C>T

Variant summary

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

The NM_001740.5(CALB2):​c.95-272C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,086 control chromosomes in the GnomAD database, including 5,064 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 0.23 (5064 hom., cov: 32)
• Consequence: CALB2 NM_001740.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

Genes affected

CALB2 (HGNC:1435): (calbindin 2) This gene encodes an intracellular calcium-binding protein belonging to the troponin C superfamily. Members of this protein family have six EF-hand domains which bind calcium. This protein plays a role in diverse cellular functions, including message targeting and intracellular calcium buffering. It also functions as a modulator of neuronal excitability, and is a diagnostic marker for some human diseases, including Hirschsprung disease and some cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010]

LINC02136 (HGNC:52995): (long intergenic non-protein coding RNA 2136)

LOC105371332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001740.5. 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
	CALB2	NM_001740.5	MANE Select	c.95-272C>T		intron	N/A	NP_001731.2
	CALB2	NM_007088.4		c.95-272C>T		intron	N/A	NP_009019.1
	CALB2	NR_027910.3		n.165-272C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALB2	ENST00000302628.9	TSL:1 MANE Select	c.95-272C>T		intron	N/A	ENSP00000307508.4
	CALB2	ENST00000562305.5	TSL:3	c.92-272C>T		intron	N/A	ENSP00000454639.1
	CALB2	ENST00000349553.9	TSL:5	c.95-272C>T		intron	N/A	ENSP00000340294.5

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35447 AN: 151968 Hom.: 5064 Cov.: 32

Gnomad AFR AF: 0.0621

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.241

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.233 AC: 35457 AN: 152086 Hom.: 5064 Cov.: 32 AF XY: 0.234 AC XY: 17364 AN XY: 74340

African (AFR) AF: 0.0621 AC: 2577 AN: 41522

American (AMR) AF: 0.270 AC: 4122 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 987 AN: 3466

East Asian (EAS) AF: 0.241 AC: 1243 AN: 5158

South Asian (SAS) AF: 0.384 AC: 1849 AN: 4816

European-Finnish (FIN) AF: 0.271 AC: 2858 AN: 10556

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21043 AN: 67972

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.248 Hom.: 678

Bravo AF: 0.223

Asia WGS AF: 0.300 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.44
PhyloP100		-1.1
PromoterAI		-0.014	Neutral
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: rs1800642; hg19: chr16-71405784;