rs11274804

Variant names:

• chr2-40255057-T-TTCATCCCCTCTCCA
• rs11274804
• NM_021097.5:c.1809-76565_1809-76564insTGGAGAGGGGATGA

Your query was ambiguous. Multiple possible variants found:

• chr2-40255057-T-TTCATCCCCTCTCCA
• chr2-40255057-T-TTCATTCCCTCTCCA
• chr2-40255057-T-TTCATTCCCTCTTCTTTGCTTTTTATTTCTTTCTCCTTCATTCCCTCTCCA
• chr2-40255057-T-TTTATTCCCTCTCCA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_021097.5(SLC8A1):​c.1809-76565_1809-76564insTGGAGAGGGGATGA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 30)
• Consequence: SLC8A1 NM_021097.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 1 publications found

Genes affected

SLC8A1 (HGNC:11068): (solute carrier family 8 member A1) In cardiac myocytes, Ca(2+) concentrations alternate between high levels during contraction and low levels during relaxation. The increase in Ca(2+) concentration during contraction is primarily due to release of Ca(2+) from intracellular stores. However, some Ca(2+) also enters the cell through the sarcolemma (plasma membrane). During relaxation, Ca(2+) is sequestered within the intracellular stores. To prevent overloading of intracellular stores, the Ca(2+) that entered across the sarcolemma must be extruded from the cell. The Na(+)-Ca(2+) exchanger is the primary mechanism by which the Ca(2+) is extruded from the cell during relaxation. In the heart, the exchanger may play a key role in digitalis action. The exchanger is the dominant mechanism in returning the cardiac myocyte to its resting state following excitation.[supplied by OMIM, Apr 2004]

SLC8A1-AS1 (HGNC:44102): (SLC8A1 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021097.5. 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
	SLC8A1	NM_021097.5	MANE Select	c.1809-76565_1809-76564insTGGAGAGGGGATGA		intron	N/A	NP_066920.1
	SLC8A1	NM_001372263.2		c.1809-76565_1809-76564insTGGAGAGGGGATGA		intron	N/A	NP_001359192.1
	SLC8A1	NM_001394103.1		c.1809-76565_1809-76564insTGGAGAGGGGATGA		intron	N/A	NP_001381032.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC8A1	ENST00000332839.9	TSL:1 MANE Select	c.1809-76565_1809-76564insTGGAGAGGGGATGA		intron	N/A	ENSP00000332931.4
	SLC8A1	ENST00000403092.5	TSL:1	c.1809-76565_1809-76564insTGGAGAGGGGATGA		intron	N/A	ENSP00000384763.1
	SLC8A1	ENST00000405901.7	TSL:1	c.1809-76565_1809-76564insTGGAGAGGGGATGA		intron	N/A	ENSP00000385678.3

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 17

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs11274804; hg19: chr2-40482197;