rs2986034

Variant names:

• chr10-103472823-G-A
• rs2986034
• NM_001129742.2:c.*390C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-103472823-G-A
• chr10-103472823-G-C

Variant summary

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

The NM_001129742.2(CALHM3):​c.*390C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.719 in 181,208 control chromosomes in the GnomAD database, including 47,727 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 0.71 (39454 hom., cov: 31)
  • Exomes 𝑓: 0.74 (8273 hom.)
• Consequence: CALHM3 NM_001129742.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 7 publications found

Genes affected

CALHM3 (HGNC:23458): (calcium homeostasis modulator 3) Predicted to enable cation channel activity. Predicted to be involved in ATP transport. Predicted to be located in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CALHM3	NM_001129742.2	c.*390C>T		3_prime_UTR_variant	Exon 3 of 3	ENST00000369783.4	NP_001123214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CALHM3	ENST00000369783.4	c.*390C>T		3_prime_UTR_variant	Exon 3 of 3	1	NM_001129742.2	ENSP00000358798.4

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108612 AN: 151964 Hom.: 39435 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.728

GnomAD4 exome AF: 0.743 AC: 21627 AN: 29126 Hom.: 8273 Cov.: 0 AF XY: 0.745 AC XY: 10760 AN XY: 14448

African (AFR) AF: 0.567 AC: 740 AN: 1304

American (AMR) AF: 0.809 AC: 688 AN: 850

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 958 AN: 1280

East Asian (EAS) AF: 0.840 AC: 1449 AN: 1726

South Asian (SAS) AF: 0.909 AC: 269 AN: 296

European-Finnish (FIN) AF: 0.762 AC: 972 AN: 1276

Middle Eastern (MID) AF: 0.720 AC: 121 AN: 168

European-Non Finnish (NFE) AF: 0.739 AC: 14926 AN: 20184

Other (OTH) AF: 0.737 AC: 1504 AN: 2042

GnomAD4 genome AF: 0.715 AC: 108676 AN: 152082 Hom.: 39454 Cov.: 31 AF XY: 0.720 AC XY: 53515 AN XY: 74352

African (AFR) AF: 0.582 AC: 24100 AN: 41438

American (AMR) AF: 0.785 AC: 12005 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3468

East Asian (EAS) AF: 0.790 AC: 4090 AN: 5176

South Asian (SAS) AF: 0.858 AC: 4137 AN: 4820

European-Finnish (FIN) AF: 0.791 AC: 8374 AN: 10592

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51032 AN: 67982

Other (OTH) AF: 0.730 AC: 1541 AN: 2110

Alfa AF: 0.740 Hom.: 53224

Bravo AF: 0.708

Asia WGS AF: 0.834 AC: 2900 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	0.40
DANN	Benign	0.37
PhyloP100		0.16
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: rs2986034; hg19: chr10-105232580;