3-36515233-T-C

Variant names:

• chr3-36515233-T-C
• rs6797696
• NM_003149.3:c.920+9399T>C

Variant summary

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

The NM_003149.3(STAC):​c.920+9399T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,828 control chromosomes in the GnomAD database, including 39,684 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 0.72 (39684 hom., cov: 29)
• Consequence: STAC NM_003149.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 3 publications found

Genes affected

STAC (HGNC:11353): (SH3 and cysteine rich domain) Predicted to enable transmembrane transporter binding activity. Predicted to be involved in positive regulation of protein localization to plasma membrane; positive regulation of voltage-gated calcium channel activity; and skeletal muscle contraction. Predicted to act upstream of or within cellular response to heat; muscle contraction; and regulation of voltage-gated calcium channel activity. Predicted to be located in T-tubule. Predicted to be extrinsic component of cytoplasmic side 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003149.3. 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
	STAC	NM_003149.3	MANE Select	c.920+9399T>C		intron	N/A	NP_003140.1	Q99469
	STAC	NM_001292049.2		c.737+9399T>C		intron	N/A	NP_001278978.1	E9PEA7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAC	ENST00000273183.8	TSL:1 MANE Select	c.920+9399T>C		intron	N/A	ENSP00000273183.3	Q99469
	STAC	ENST00000903142.1		c.887+9399T>C		intron	N/A	ENSP00000573201.1
	STAC	ENST00000457375.6	TSL:2	c.737+9399T>C		intron	N/A	ENSP00000393713.2	E9PEA7

Frequencies

GnomAD3 genomes AF: 0.720 AC: 109271 AN: 151710 Hom.: 39644 Cov.: 29

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.763

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.719

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.720 AC: 109367 AN: 151828 Hom.: 39684 Cov.: 29 AF XY: 0.720 AC XY: 53433 AN XY: 74176

African (AFR) AF: 0.779 AC: 32245 AN: 41410

American (AMR) AF: 0.777 AC: 11833 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 2293 AN: 3468

East Asian (EAS) AF: 0.763 AC: 3927 AN: 5150

South Asian (SAS) AF: 0.619 AC: 2974 AN: 4804

European-Finnish (FIN) AF: 0.689 AC: 7253 AN: 10528

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.685 AC: 46538 AN: 67918

Other (OTH) AF: 0.720 AC: 1520 AN: 2112

Alfa AF: 0.699 Hom.: 63014

Bravo AF: 0.734

Asia WGS AF: 0.719 AC: 2499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.33
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: rs6797696; hg19: chr3-36556725;