rs523516

Variant names:

• chr17-39175092-A-C
• rs523516
• NM_000723.5:c.*101T>G

Your query was ambiguous. Multiple possible variants found:

• chr17-39175092-A-C
• chr17-39175092-A-G
• chr17-39175092-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_000723.5(CACNB1):​c.*101T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000246 in 814,480 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: CACNB1 NM_000723.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 16 publications found

Genes affected

CACNB1 (HGNC:1401): (calcium voltage-gated channel auxiliary subunit beta 1) The protein encoded by this gene belongs to the calcium channel beta subunit family. It plays an important role in the calcium channel by modulating G protein inhibition, increasing peak calcium current, controlling the alpha-1 subunit membrane targeting and shifting the voltage dependence of activation and inactivation. Alternative splicing occurs at this locus and three transcript variants encoding three distinct isoforms have been identified. [provided by RefSeq, Jul 2008]

ENSG00000266101 (HGNC:58562):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000723.5. 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
	CACNB1	NM_000723.5	MANE Select	c.*101T>G		3_prime_UTR	Exon 14 of 14	NP_000714.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNB1	ENST00000394303.8	TSL:1 MANE Select	c.*101T>G		3_prime_UTR	Exon 14 of 14	ENSP00000377840.3	Q02641-1
	CACNB1	ENST00000539338.6	TSL:1	n.4017T>G		non_coding_transcript_exon	Exon 12 of 12
	CACNB1	ENST00000910733.1		c.*101T>G		3_prime_UTR	Exon 14 of 14	ENSP00000580792.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000246 AC: 2 AN: 814480 Hom.: 0 Cov.: 11 AF XY: 0.00000479 AC XY: 2 AN XY: 417392

African (AFR) AF: 0.00 AC: 0 AN: 19842

American (AMR) AF: 0.00 AC: 0 AN: 27660

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16406

East Asian (EAS) AF: 0.00 AC: 0 AN: 36340

South Asian (SAS) AF: 0.00 AC: 0 AN: 58660

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46296

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2688

European-Non Finnish (NFE) AF: 0.00000352 AC: 2 AN: 568694

Other (OTH) AF: 0.00 AC: 0 AN: 37894

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 107

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.2
DANN	Benign	0.74
PhyloP100		0.42

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: rs523516; hg19: chr17-37331345;