16-71371881-C-T

Position:

• chr16-71371881-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CALB2	NM_001740.5	c.95-272C>T		intron_variant		ENST00000302628.9
LOC105371332	XR_933714.3	n.458+2621G>A		intron_variant, non_coding_transcript_variant
CALB2	NM_007088.4	c.95-272C>T		intron_variant
CALB2	NR_027910.3	n.165-272C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CALB2	ENST00000302628.9	c.95-272C>T		intron_variant		1	NM_001740.5	P1
LINC02136	ENST00000567469.2	n.705+2621G>A		intron_variant, non_coding_transcript_variant		4
CALB2	ENST00000349553.9	c.95-272C>T		intron_variant		5
CALB2	ENST00000562305.5	c.94-272C>T		intron_variant		3

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

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.275

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.44

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

Other links and lift over

dbSNP: rs1800642; hg19: chr16-71405784;