rs370103843

Variant names:

• chr7-82066526-TAAAAA-T
• NM_000722.4:c.659-7_659-3delTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr7-82066526-TAAAAA-T
• chr7-82066526-TAAAAA-TA
• chr7-82066526-TAAAAA-TAA
• chr7-82066526-TAAAAA-TAAA
• chr7-82066526-TAAAAA-TAAAA
• chr7-82066526-TAAAAA-TAAAAAA
• chr7-82066526-TAAAAA-TAAAAAAA
• chr7-82066526-TAAAAA-TAAAAAAAA
• chr7-82066526-TAAAAA-TAAAAAAAAA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_000722.4(CACNA2D1):​c.659-7_659-3delTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,336,788 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 27)
  • Exomes 𝑓: 0.000033 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CACNA2D1 NM_000722.4 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51

Genes affected

CACNA2D1 (HGNC:1399): (calcium voltage-gated channel auxiliary subunit alpha2delta 1) The preproprotein encoded by this gene is cleaved into multiple chains that comprise the alpha-2 and delta subunits of the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. Mutations in this gene can cause cardiac deficiencies, including Brugada syndrome and short QT syndrome. Alternate splicing results in multiple transcript variants, some of which may lack the delta subunit portion. [provided by RefSeq, Nov 2014]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAdExome4 at 44 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA2D1	NM_000722.4	c.659-7_659-3delTTTTT		splice_region_variant, intron_variant	Intron 7 of 38	ENST00000356860.8	NP_000713.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA2D1	ENST00000356860.8	c.659-7_659-3delTTTTT		splice_region_variant, intron_variant	Intron 7 of 38	1	NM_000722.4	ENSP00000349320.3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 111752 Hom.: 0 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000329 AC: 44 AN: 1336788 Hom.: 0 AF XY: 0.0000318 AC XY: 21 AN XY: 660438

Gnomad4 AFR exome AF: 0.000141

Gnomad4 AMR exome AF: 0.000267

Gnomad4 ASJ exome AF: 0.0000425

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000714

Gnomad4 FIN exome AF: 0.000102

Gnomad4 NFE exome AF: 0.0000200

Gnomad4 OTH exome AF: 0.0000181

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 111752 Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0 AN XY: 52976

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-81695842;